data_1T1O
#
_entry.id 1T1O
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.386
_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
#
loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB 1T1O pdb_00001t1o 10.2210/pdb1t1o/pdb
RCSB RCSB022199 ? ?
WWPDB D_1000022199 ? ?
#
loop_
_pdbx_audit_revision_history.ordinal
_pdbx_audit_revision_history.data_content_type
_pdbx_audit_revision_history.major_revision
_pdbx_audit_revision_history.minor_revision
_pdbx_audit_revision_history.revision_date
1 'Structure model' 1 0 2004-06-15
2 'Structure model' 1 1 2008-04-30
3 'Structure model' 1 2 2011-07-13
4 'Structure model' 1 3 2024-02-14
#
_pdbx_audit_revision_details.ordinal 1
_pdbx_audit_revision_details.revision_ordinal 1
_pdbx_audit_revision_details.data_content_type 'Structure model'
_pdbx_audit_revision_details.provider repository
_pdbx_audit_revision_details.type 'Initial release'
_pdbx_audit_revision_details.description ?
_pdbx_audit_revision_details.details ?
#
loop_
_pdbx_audit_revision_group.ordinal
_pdbx_audit_revision_group.revision_ordinal
_pdbx_audit_revision_group.data_content_type
_pdbx_audit_revision_group.group
1 2 'Structure model' 'Version format compliance'
2 3 'Structure model' 'Version format compliance'
3 4 'Structure model' 'Data collection'
4 4 'Structure model' 'Database references'
5 4 'Structure model' 'Refinement description'
#
loop_
_pdbx_audit_revision_category.ordinal
_pdbx_audit_revision_category.revision_ordinal
_pdbx_audit_revision_category.data_content_type
_pdbx_audit_revision_category.category
1 4 'Structure model' chem_comp_atom
2 4 'Structure model' chem_comp_bond
3 4 'Structure model' database_2
4 4 'Structure model' em_3d_fitting_list
5 4 'Structure model' em_image_scans
6 4 'Structure model' pdbx_initial_refinement_model
#
loop_
_pdbx_audit_revision_item.ordinal
_pdbx_audit_revision_item.revision_ordinal
_pdbx_audit_revision_item.data_content_type
_pdbx_audit_revision_item.item
1 4 'Structure model' '_database_2.pdbx_DOI'
2 4 'Structure model' '_database_2.pdbx_database_accession'
3 4 'Structure model' '_em_3d_fitting_list.accession_code'
4 4 'Structure model' '_em_3d_fitting_list.initial_refinement_model_id'
5 4 'Structure model' '_em_3d_fitting_list.source_name'
6 4 'Structure model' '_em_3d_fitting_list.type'
#
_pdbx_database_status.entry_id 1T1O
_pdbx_database_status.status_code REL
_pdbx_database_status.recvd_initial_deposition_date 2004-04-16
_pdbx_database_status.deposit_site RCSB
_pdbx_database_status.process_site RCSB
_pdbx_database_status.SG_entry .
_pdbx_database_status.status_code_sf ?
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.pdb_format_compatible Y
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.status_code_nmr_data ?
_pdbx_database_status.methods_development_category ?
#
loop_
_pdbx_database_related.db_name
_pdbx_database_related.db_id
_pdbx_database_related.details
_pdbx_database_related.content_type
PDB 1KC9 'X-ray crystallographic Structure of the 50S ribosomal subunit from D. radiodurans' unspecified
PDB 1FJF 'X-ray crystallographic Structure of the 30S ribosomal subunit from T. thermophilu' unspecified
PDB 1T1M . unspecified
EMDB EMD-1077 . 'associated EM volume'
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
'Agrawal, R.K.' 1
'Sharma, M.R.' 2
'Kiel, M.C.' 3
'Hirokawa, G.' 4
'Booth, T.M.' 5
'Spahn, C.M.' 6
'Grassucci, R.A.' 7
'Kaji, A.' 8
'Frank, J.' 9
#
loop_
_citation.id
_citation.title
_citation.journal_abbrev
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.year
_citation.journal_id_ASTM
_citation.country
_citation.journal_id_ISSN
_citation.journal_id_CSD
_citation.book_publisher
_citation.pdbx_database_id_PubMed
_citation.pdbx_database_id_DOI
primary 'Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: Functional implications'
Proc.Natl.Acad.Sci.USA 101 8900 8905 2004 PNASA6 US 0027-8424 0040 ? 15178758 10.1073/pnas.0401904101
1 'High resolution structure of the large ribosomal subunit from a mesophilic eubacterium'
'Cell(Cambridge,Mass.)' 107 679 688 2001 CELLB5 US 0092-8674 0998 ? 11733066 '10.1016/S0092-8674(01)00546-3'
2 'Structure of the 30S ribosomal subunit' Nature 407 327
339 2000 NATUAS UK 0028-0836 0006 ? 11014182 10.1038/35030006
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary 'Agrawal, R.K.' 1 ?
primary 'Sharma, M.R.' 2 ?
primary 'Kiel, M.C.' 3 ?
primary 'Hirokawa, G.' 4 ?
primary 'Booth, T.M.' 5 ?
primary 'Spahn, C.M.' 6 ?
primary 'Grassucci, R.A.' 7 ?
primary 'Kaji, A.' 8 ?
primary 'Frank, J.' 9 ?
1 'Harms, J.' 10 ?
1 'Schluenzen, F.' 11 ?
1 'Zarivach, R.' 12 ?
1 'Bashan, A.' 13 ?
1 'Gat, S.' 14 ?
1 'Agmon, I.' 15 ?
1 'Bartels, H.' 16 ?
1 'Franceschi, F.' 17 ?
1 'Yonath, A.' 18 ?
2 'Wimberly, B.T.' 19 ?
2 'Brodersen, D.E.' 20 ?
2 'Clemons Jr., W.M.' 21 ?
2 'Morgan-Warren, R.J.' 22 ?
2 'Carter, A.P.' 23 ?
2 'Vonrhein, C.' 24 ?
2 'Hartsch, T.' 25 ?
2 'Ramakrishnan, V.' 26 ?
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1 polymer nat 'dodecamer fragment of double helix from 23S rRNA' 3852.344 1 ? ? 'Apical loop of Helix 43'
'fitted into the cryo-EM map of the 70S ribosome'
2 polymer nat '19-mer fragment of the 23S rRNA' 6077.673 1 ? ? 'Helix 69'
'fitted into the cryo-EM map of the 70S ribosome'
3 polymer nat '42-mer fragment of double helix from 16S rRNA' 13581.124 1 ? ? 'Top portion of helix 44'
'fitted into the cryo-EM map of the 70S ribosome'
#
_entity_name_com.entity_id 3
_entity_name_com.name 'Ribosome releasing factor; RRF'
#
loop_
_entity_poly.entity_id
_entity_poly.type
_entity_poly.nstd_linkage
_entity_poly.nstd_monomer
_entity_poly.pdbx_seq_one_letter_code
_entity_poly.pdbx_seq_one_letter_code_can
_entity_poly.pdbx_strand_id
_entity_poly.pdbx_target_identifier
1 polyribonucleotide no no UGGCUUAGAAGC UGGCUUAGAAGC A ?
2 polyribonucleotide no no GGCCGUAACUAUAACGGUC GGCCGUAACUAUAACGGUC B ?
3 polyribonucleotide no no GCCCGUCACACCAUGGGAGUAUGACUGGGGUGAAGUCGUAAC GCCCGUCACACCAUGGGAGUAUGACUGGGGUGAAGUCGUAAC C ?
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 U n
1 2 G n
1 3 G n
1 4 C n
1 5 U n
1 6 U n
1 7 A n
1 8 G n
1 9 A n
1 10 A n
1 11 G n
1 12 C n
2 1 G n
2 2 G n
2 3 C n
2 4 C n
2 5 G n
2 6 U n
2 7 A n
2 8 A n
2 9 C n
2 10 U n
2 11 A n
2 12 U n
2 13 A n
2 14 A n
2 15 C n
2 16 G n
2 17 G n
2 18 U n
2 19 C n
3 1 G n
3 2 C n
3 3 C n
3 4 C n
3 5 G n
3 6 U n
3 7 C n
3 8 A n
3 9 C n
3 10 A n
3 11 C n
3 12 C n
3 13 A n
3 14 U n
3 15 G n
3 16 G n
3 17 G n
3 18 A n
3 19 G n
3 20 U n
3 21 A n
3 22 U n
3 23 G n
3 24 A n
3 25 C n
3 26 U n
3 27 G n
3 28 G n
3 29 G n
3 30 G n
3 31 U n
3 32 G n
3 33 A n
3 34 A n
3 35 G n
3 36 U n
3 37 C n
3 38 G n
3 39 U n
3 40 A n
3 41 A n
3 42 C n
#
loop_
_entity_src_nat.entity_id
_entity_src_nat.pdbx_src_id
_entity_src_nat.pdbx_alt_source_flag
_entity_src_nat.pdbx_beg_seq_num
_entity_src_nat.pdbx_end_seq_num
_entity_src_nat.common_name
_entity_src_nat.pdbx_organism_scientific
_entity_src_nat.pdbx_ncbi_taxonomy_id
_entity_src_nat.genus
_entity_src_nat.species
_entity_src_nat.strain
_entity_src_nat.tissue
_entity_src_nat.tissue_fraction
_entity_src_nat.pdbx_secretion
_entity_src_nat.pdbx_fragment
_entity_src_nat.pdbx_variant
_entity_src_nat.pdbx_cell_line
_entity_src_nat.pdbx_atcc
_entity_src_nat.pdbx_cellular_location
_entity_src_nat.pdbx_organ
_entity_src_nat.pdbx_organelle
_entity_src_nat.pdbx_cell
_entity_src_nat.pdbx_plasmid_name
_entity_src_nat.pdbx_plasmid_details
_entity_src_nat.details
1 1 sample ? ? ? 'Escherichia coli' 562 Escherichia ? MRE600 ? ? ? ? ? ? ? ? ? ? ? ? ? ?
2 1 sample ? ? ? 'Escherichia coli' 562 Escherichia ? MRE600 ? ? ? ? ? ? ? ? ? ? ? ? ? ?
3 1 sample ? ? ? 'Escherichia coli' 562 Escherichia ? MRE600 ? ? ? ? ? ? ? ? ? ? ? ? ? ?
#
loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221
C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197
G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221
U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181
#
loop_
_pdbx_poly_seq_scheme.asym_id
_pdbx_poly_seq_scheme.entity_id
_pdbx_poly_seq_scheme.seq_id
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.ndb_seq_num
_pdbx_poly_seq_scheme.pdb_seq_num
_pdbx_poly_seq_scheme.auth_seq_num
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_poly_seq_scheme.auth_mon_id
_pdbx_poly_seq_scheme.pdb_strand_id
_pdbx_poly_seq_scheme.pdb_ins_code
_pdbx_poly_seq_scheme.hetero
A 1 1 U 1 1061 1061 U U A . n
A 1 2 G 2 1062 1062 G G A . n
A 1 3 G 3 1063 1063 G G A . n
A 1 4 C 4 1064 1064 C C A . n
A 1 5 U 5 1065 1065 U U A . n
A 1 6 U 6 1066 1066 U U A . n
A 1 7 A 7 1067 1067 A A A . n
A 1 8 G 8 1068 1068 G G A . n
A 1 9 A 9 1069 1069 A A A . n
A 1 10 A 10 1070 1070 A A A . n
A 1 11 G 11 1071 1071 G G A . n
A 1 12 C 12 1072 1072 C C A . n
B 2 1 G 1 1906 1906 G G B . n
B 2 2 G 2 1907 1907 G G B . n
B 2 3 C 3 1908 1908 C C B . n
B 2 4 C 4 1909 1909 C C B . n
B 2 5 G 5 1910 1910 G G B . n
B 2 6 U 6 1911 1911 U U B . n
B 2 7 A 7 1912 1912 A A B . n
B 2 8 A 8 1913 1913 A A B . n
B 2 9 C 9 1914 1914 C C B . n
B 2 10 U 10 1915 1915 U U B . n
B 2 11 A 11 1916 1916 A A B . n
B 2 12 U 12 1917 1917 U U B . n
B 2 13 A 13 1918 1918 A A B . n
B 2 14 A 14 1919 1919 A A B . n
B 2 15 C 15 1920 1920 C C B . n
B 2 16 G 16 1921 1921 G G B . n
B 2 17 G 17 1922 1922 G G B . n
B 2 18 U 18 1923 1923 U U B . n
B 2 19 C 19 1924 1924 C C B . n
C 3 1 G 1 1401 1401 G G C . n
C 3 2 C 2 1402 1402 C C C . n
C 3 3 C 3 1403 1403 C C C . n
C 3 4 C 4 1404 1404 C C C . n
C 3 5 G 5 1405 1405 G G C . n
C 3 6 U 6 1406 1406 U U C . n
C 3 7 C 7 1407 1407 C C C . n
C 3 8 A 8 1408 1408 A A C . n
C 3 9 C 9 1409 1409 C C C . n
C 3 10 A 10 1410 1410 A A C . n
C 3 11 C 11 1411 1411 C C C . n
C 3 12 C 12 1412 1412 C C C . n
C 3 13 A 13 1413 1413 A A C . n
C 3 14 U 14 1414 1414 U U C . n
C 3 15 G 15 1415 1415 G G C . n
C 3 16 G 16 1416 1416 G G C . n
C 3 17 G 17 1417 1417 G G C . n
C 3 18 A 18 1418 1418 A A C . n
C 3 19 G 19 1419 1419 G G C . n
C 3 20 U 20 1420 1420 U U C . n
C 3 21 A 21 1480 1480 A A C . n
C 3 22 U 22 1481 1481 U U C . n
C 3 23 G 23 1482 1482 G G C . n
C 3 24 A 24 1483 1483 A A C . n
C 3 25 C 25 1484 1484 C C C . n
C 3 26 U 26 1485 1485 U U C . n
C 3 27 G 27 1486 1486 G G C . n
C 3 28 G 28 1487 1487 G G C . n
C 3 29 G 29 1488 1488 G G C . n
C 3 30 G 30 1489 1489 G G C . n
C 3 31 U 31 1490 1490 U U C . n
C 3 32 G 32 1491 1491 G G C . n
C 3 33 A 33 1492 1492 A A C . n
C 3 34 A 34 1493 1493 A A C . n
C 3 35 G 35 1494 1494 G G C . n
C 3 36 U 36 1495 1495 U U C . n
C 3 37 C 37 1496 1496 C C C . n
C 3 38 G 38 1497 1497 G G C . n
C 3 39 U 39 1498 1498 U U C . n
C 3 40 A 40 1499 1499 A A C . n
C 3 41 A 41 1500 1500 A A C . n
C 3 42 C 42 1501 1501 C C C . n
#
_exptl.entry_id 1T1O
_exptl.method 'ELECTRON MICROSCOPY'
_exptl.crystals_number ?
#
_refine_hist.pdbx_refine_id 'ELECTRON MICROSCOPY'
_refine_hist.cycle_id LAST
_refine_hist.pdbx_number_atoms_protein 0
_refine_hist.pdbx_number_atoms_nucleic_acid 73
_refine_hist.pdbx_number_atoms_ligand 0
_refine_hist.number_atoms_solvent 0
_refine_hist.number_atoms_total 73
_refine_hist.d_res_high .
_refine_hist.d_res_low .
#
_struct.entry_id 1T1O
_struct.title 'Components of the control 70S ribosome to provide reference for the RRF binding site'
_struct.pdbx_model_details ?
_struct.pdbx_CASP_flag ?
_struct.pdbx_model_type_details ?
#
_struct_keywords.entry_id 1T1O
_struct_keywords.pdbx_keywords RIBOSOME
_struct_keywords.text 'RRF binding position on the ribosome, RIBOSOME'
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 2 ?
C N N 3 ?
#
loop_
_struct_ref.id
_struct_ref.entity_id
_struct_ref.db_name
_struct_ref.db_code
_struct_ref.pdbx_db_accession
_struct_ref.pdbx_db_isoform
_struct_ref.pdbx_seq_one_letter_code
_struct_ref.pdbx_align_begin
1 1 PDB 1T1O 1T1O ? ? ?
2 2 PDB 1T1O 1T1O ? ? ?
3 3 PDB 1T1O 1T1O ? ? ?
#
loop_
_struct_ref_seq.align_id
_struct_ref_seq.ref_id
_struct_ref_seq.pdbx_PDB_id_code
_struct_ref_seq.pdbx_strand_id
_struct_ref_seq.seq_align_beg
_struct_ref_seq.pdbx_seq_align_beg_ins_code
_struct_ref_seq.seq_align_end
_struct_ref_seq.pdbx_seq_align_end_ins_code
_struct_ref_seq.pdbx_db_accession
_struct_ref_seq.db_align_beg
_struct_ref_seq.pdbx_db_align_beg_ins_code
_struct_ref_seq.db_align_end
_struct_ref_seq.pdbx_db_align_end_ins_code
_struct_ref_seq.pdbx_auth_seq_align_beg
_struct_ref_seq.pdbx_auth_seq_align_end
1 1 1T1O A 1 ? 12 ? 1T1O 1061 ? 1072 ? 1061 1072
2 2 1T1O B 1 ? 19 ? 1T1O 1906 ? 1924 ? 1906 1924
3 3 1T1O C 1 ? 42 ? 1T1O 1401 ? 1501 ? 1401 1501
#
_pdbx_struct_assembly.id 1
_pdbx_struct_assembly.details author_defined_assembly
_pdbx_struct_assembly.method_details ?
_pdbx_struct_assembly.oligomeric_details trimeric
_pdbx_struct_assembly.oligomeric_count 3
#
_pdbx_struct_assembly_gen.assembly_id 1
_pdbx_struct_assembly_gen.oper_expression 1
_pdbx_struct_assembly_gen.asym_id_list A,B,C
#
_pdbx_struct_oper_list.id 1
_pdbx_struct_oper_list.type 'identity operation'
_pdbx_struct_oper_list.name 1_555
_pdbx_struct_oper_list.symmetry_operation x,y,z
_pdbx_struct_oper_list.matrix[1][1] 1.0000000000
_pdbx_struct_oper_list.matrix[1][2] 0.0000000000
_pdbx_struct_oper_list.matrix[1][3] 0.0000000000
_pdbx_struct_oper_list.vector[1] 0.0000000000
_pdbx_struct_oper_list.matrix[2][1] 0.0000000000
_pdbx_struct_oper_list.matrix[2][2] 1.0000000000
_pdbx_struct_oper_list.matrix[2][3] 0.0000000000
_pdbx_struct_oper_list.vector[2] 0.0000000000
_pdbx_struct_oper_list.matrix[3][1] 0.0000000000
_pdbx_struct_oper_list.matrix[3][2] 0.0000000000
_pdbx_struct_oper_list.matrix[3][3] 1.0000000000
_pdbx_struct_oper_list.vector[3] 0.0000000000
#
_struct_biol.id 1
_struct_biol.pdbx_parent_biol_id ?
_struct_biol.details ?
#
_em_3d_fitting.id 1
_em_3d_fitting.entry_id 1T1O
_em_3d_fitting.ref_protocol OTHER
_em_3d_fitting.ref_space ?
_em_3d_fitting.overall_b_value ?
_em_3d_fitting.target_criteria ?
_em_3d_fitting.details 'METHOD--Cross corelation coefficient based manual fitting in O'
_em_3d_fitting.method ?
#
loop_
_em_3d_fitting_list.3d_fitting_id
_em_3d_fitting_list.id
_em_3d_fitting_list.pdb_entry_id
_em_3d_fitting_list.pdb_chain_id
_em_3d_fitting_list.details
_em_3d_fitting_list.initial_refinement_model_id
_em_3d_fitting_list.chain_id
_em_3d_fitting_list.chain_residue_range
_em_3d_fitting_list.pdb_chain_residue_range
_em_3d_fitting_list.source_name
_em_3d_fitting_list.type
_em_3d_fitting_list.accession_code
1 1 1KC9 ? ? 1 ? ? ? PDB 'experimental model' 1KC9
1 2 1JFJ ? ? 2 ? ? ? PDB 'experimental model' 1JFJ
#
_em_3d_reconstruction.entry_id 1T1O
_em_3d_reconstruction.id 1
_em_3d_reconstruction.symmetry_type POINT
_em_3d_reconstruction.num_particles 51217
_em_3d_reconstruction.image_processing_id 1
_em_3d_reconstruction.method '3D projection matching; conjugate gradients with regularization'
_em_3d_reconstruction.nominal_pixel_size ?
_em_3d_reconstruction.actual_pixel_size 2.82
_em_3d_reconstruction.resolution 12
_em_3d_reconstruction.magnification_calibration TMV
_em_3d_reconstruction.details 'SPIDER package'
_em_3d_reconstruction.resolution_method ?
_em_3d_reconstruction.num_class_averages ?
_em_3d_reconstruction.algorithm ?
#
_em_buffer.id 1
_em_buffer.specimen_id 1
_em_buffer.name ?
_em_buffer.pH 7.5
_em_buffer.details ?
#
_em_entity_assembly.id 1
_em_entity_assembly.name '70S-RRF complex'
_em_entity_assembly.type RIBOSOME
_em_entity_assembly.parent_id 0
_em_entity_assembly.synonym ?
_em_entity_assembly.details ?
_em_entity_assembly.oligomeric_details ?
#
_em_imaging.entry_id 1T1O
_em_imaging.id 1
_em_imaging.specimen_id 1
_em_imaging.date 2002-06-01
_em_imaging.temperature 93
_em_imaging.microscope_model 'FEI TECNAI F20'
_em_imaging.nominal_defocus_min 1400
_em_imaging.nominal_defocus_max 4400
_em_imaging.tilt_angle_min 0
_em_imaging.tilt_angle_max 0
_em_imaging.nominal_cs 2.0
_em_imaging.mode 'BRIGHT FIELD'
_em_imaging.illumination_mode 'FLOOD BEAM'
_em_imaging.nominal_magnification 50000
_em_imaging.calibrated_magnification 49696
_em_imaging.electron_source 'FIELD EMISSION GUN'
_em_imaging.accelerating_voltage 200
_em_imaging.details ?
_em_imaging.specimen_holder_type ?
_em_imaging.specimen_holder_model ?
_em_imaging.citation_id ?
_em_imaging.detector_distance ?
_em_imaging.recording_temperature_maximum ?
_em_imaging.recording_temperature_minimum ?
_em_imaging.astigmatism ?
_em_imaging.electron_beam_tilt_params ?
#
_em_sample_support.id 1
_em_sample_support.specimen_id 1
_em_sample_support.details 'Quantifoil holley-carbon film grids'
_em_sample_support.film_material ?
_em_sample_support.grid_material ?
_em_sample_support.grid_mesh_size ?
_em_sample_support.grid_type ?
_em_sample_support.method ?
#
_em_vitrification.entry_id 1T1O
_em_vitrification.id 1
_em_vitrification.instrument 'HOMEMADE PLUNGER'
_em_vitrification.cryogen_name ETHANE
_em_vitrification.details 'Rapid-freezing in liquid ethane'
_em_vitrification.citation_id ?
_em_vitrification.humidity ?
_em_vitrification.method ?
_em_vitrification.specimen_id 1
_em_vitrification.temp ?
_em_vitrification.time_resolved_state ?
#
_em_experiment.entry_id 1T1O
_em_experiment.id 1
_em_experiment.aggregation_state PARTICLE
_em_experiment.entity_assembly_id 1
_em_experiment.reconstruction_method 'SINGLE PARTICLE'
#
_em_single_particle_entity.entry_id 1T1O
_em_single_particle_entity.id 1
_em_single_particle_entity.point_symmetry C1
_em_single_particle_entity.image_processing_id 1
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_ordinal
A OP3 O N N 1
A P P N N 2
A OP1 O N N 3
A OP2 O N N 4
A "O5'" O N N 5
A "C5'" C N N 6
A "C4'" C N R 7
A "O4'" O N N 8
A "C3'" C N S 9
A "O3'" O N N 10
A "C2'" C N R 11
A "O2'" O N N 12
A "C1'" C N R 13
A N9 N Y N 14
A C8 C Y N 15
A N7 N Y N 16
A C5 C Y N 17
A C6 C Y N 18
A N6 N N N 19
A N1 N Y N 20
A C2 C Y N 21
A N3 N Y N 22
A C4 C Y N 23
A HOP3 H N N 24
A HOP2 H N N 25
A "H5'" H N N 26
A "H5''" H N N 27
A "H4'" H N N 28
A "H3'" H N N 29
A "HO3'" H N N 30
A "H2'" H N N 31
A "HO2'" H N N 32
A "H1'" H N N 33
A H8 H N N 34
A H61 H N N 35
A H62 H N N 36
A H2 H N N 37
C OP3 O N N 38
C P P N N 39
C OP1 O N N 40
C OP2 O N N 41
C "O5'" O N N 42
C "C5'" C N N 43
C "C4'" C N R 44
C "O4'" O N N 45
C "C3'" C N S 46
C "O3'" O N N 47
C "C2'" C N R 48
C "O2'" O N N 49
C "C1'" C N R 50
C N1 N N N 51
C C2 C N N 52
C O2 O N N 53
C N3 N N N 54
C C4 C N N 55
C N4 N N N 56
C C5 C N N 57
C C6 C N N 58
C HOP3 H N N 59
C HOP2 H N N 60
C "H5'" H N N 61
C "H5''" H N N 62
C "H4'" H N N 63
C "H3'" H N N 64
C "HO3'" H N N 65
C "H2'" H N N 66
C "HO2'" H N N 67
C "H1'" H N N 68
C H41 H N N 69
C H42 H N N 70
C H5 H N N 71
C H6 H N N 72
G OP3 O N N 73
G P P N N 74
G OP1 O N N 75
G OP2 O N N 76
G "O5'" O N N 77
G "C5'" C N N 78
G "C4'" C N R 79
G "O4'" O N N 80
G "C3'" C N S 81
G "O3'" O N N 82
G "C2'" C N R 83
G "O2'" O N N 84
G "C1'" C N R 85
G N9 N Y N 86
G C8 C Y N 87
G N7 N Y N 88
G C5 C Y N 89
G C6 C N N 90
G O6 O N N 91
G N1 N N N 92
G C2 C N N 93
G N2 N N N 94
G N3 N N N 95
G C4 C Y N 96
G HOP3 H N N 97
G HOP2 H N N 98
G "H5'" H N N 99
G "H5''" H N N 100
G "H4'" H N N 101
G "H3'" H N N 102
G "HO3'" H N N 103
G "H2'" H N N 104
G "HO2'" H N N 105
G "H1'" H N N 106
G H8 H N N 107
G H1 H N N 108
G H21 H N N 109
G H22 H N N 110
U OP3 O N N 111
U P P N N 112
U OP1 O N N 113
U OP2 O N N 114
U "O5'" O N N 115
U "C5'" C N N 116
U "C4'" C N R 117
U "O4'" O N N 118
U "C3'" C N S 119
U "O3'" O N N 120
U "C2'" C N R 121
U "O2'" O N N 122
U "C1'" C N R 123
U N1 N N N 124
U C2 C N N 125
U O2 O N N 126
U N3 N N N 127
U C4 C N N 128
U O4 O N N 129
U C5 C N N 130
U C6 C N N 131
U HOP3 H N N 132
U HOP2 H N N 133
U "H5'" H N N 134
U "H5''" H N N 135
U "H4'" H N N 136
U "H3'" H N N 137
U "HO3'" H N N 138
U "H2'" H N N 139
U "HO2'" H N N 140
U "H1'" H N N 141
U H3 H N N 142
U H5 H N N 143
U H6 H N N 144
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
A OP3 P sing N N 1
A OP3 HOP3 sing N N 2
A P OP1 doub N N 3
A P OP2 sing N N 4
A P "O5'" sing N N 5
A OP2 HOP2 sing N N 6
A "O5'" "C5'" sing N N 7
A "C5'" "C4'" sing N N 8
A "C5'" "H5'" sing N N 9
A "C5'" "H5''" sing N N 10
A "C4'" "O4'" sing N N 11
A "C4'" "C3'" sing N N 12
A "C4'" "H4'" sing N N 13
A "O4'" "C1'" sing N N 14
A "C3'" "O3'" sing N N 15
A "C3'" "C2'" sing N N 16
A "C3'" "H3'" sing N N 17
A "O3'" "HO3'" sing N N 18
A "C2'" "O2'" sing N N 19
A "C2'" "C1'" sing N N 20
A "C2'" "H2'" sing N N 21
A "O2'" "HO2'" sing N N 22
A "C1'" N9 sing N N 23
A "C1'" "H1'" sing N N 24
A N9 C8 sing Y N 25
A N9 C4 sing Y N 26
A C8 N7 doub Y N 27
A C8 H8 sing N N 28
A N7 C5 sing Y N 29
A C5 C6 sing Y N 30
A C5 C4 doub Y N 31
A C6 N6 sing N N 32
A C6 N1 doub Y N 33
A N6 H61 sing N N 34
A N6 H62 sing N N 35
A N1 C2 sing Y N 36
A C2 N3 doub Y N 37
A C2 H2 sing N N 38
A N3 C4 sing Y N 39
C OP3 P sing N N 40
C OP3 HOP3 sing N N 41
C P OP1 doub N N 42
C P OP2 sing N N 43
C P "O5'" sing N N 44
C OP2 HOP2 sing N N 45
C "O5'" "C5'" sing N N 46
C "C5'" "C4'" sing N N 47
C "C5'" "H5'" sing N N 48
C "C5'" "H5''" sing N N 49
C "C4'" "O4'" sing N N 50
C "C4'" "C3'" sing N N 51
C "C4'" "H4'" sing N N 52
C "O4'" "C1'" sing N N 53
C "C3'" "O3'" sing N N 54
C "C3'" "C2'" sing N N 55
C "C3'" "H3'" sing N N 56
C "O3'" "HO3'" sing N N 57
C "C2'" "O2'" sing N N 58
C "C2'" "C1'" sing N N 59
C "C2'" "H2'" sing N N 60
C "O2'" "HO2'" sing N N 61
C "C1'" N1 sing N N 62
C "C1'" "H1'" sing N N 63
C N1 C2 sing N N 64
C N1 C6 sing N N 65
C C2 O2 doub N N 66
C C2 N3 sing N N 67
C N3 C4 doub N N 68
C C4 N4 sing N N 69
C C4 C5 sing N N 70
C N4 H41 sing N N 71
C N4 H42 sing N N 72
C C5 C6 doub N N 73
C C5 H5 sing N N 74
C C6 H6 sing N N 75
G OP3 P sing N N 76
G OP3 HOP3 sing N N 77
G P OP1 doub N N 78
G P OP2 sing N N 79
G P "O5'" sing N N 80
G OP2 HOP2 sing N N 81
G "O5'" "C5'" sing N N 82
G "C5'" "C4'" sing N N 83
G "C5'" "H5'" sing N N 84
G "C5'" "H5''" sing N N 85
G "C4'" "O4'" sing N N 86
G "C4'" "C3'" sing N N 87
G "C4'" "H4'" sing N N 88
G "O4'" "C1'" sing N N 89
G "C3'" "O3'" sing N N 90
G "C3'" "C2'" sing N N 91
G "C3'" "H3'" sing N N 92
G "O3'" "HO3'" sing N N 93
G "C2'" "O2'" sing N N 94
G "C2'" "C1'" sing N N 95
G "C2'" "H2'" sing N N 96
G "O2'" "HO2'" sing N N 97
G "C1'" N9 sing N N 98
G "C1'" "H1'" sing N N 99
G N9 C8 sing Y N 100
G N9 C4 sing Y N 101
G C8 N7 doub Y N 102
G C8 H8 sing N N 103
G N7 C5 sing Y N 104
G C5 C6 sing N N 105
G C5 C4 doub Y N 106
G C6 O6 doub N N 107
G C6 N1 sing N N 108
G N1 C2 sing N N 109
G N1 H1 sing N N 110
G C2 N2 sing N N 111
G C2 N3 doub N N 112
G N2 H21 sing N N 113
G N2 H22 sing N N 114
G N3 C4 sing N N 115
U OP3 P sing N N 116
U OP3 HOP3 sing N N 117
U P OP1 doub N N 118
U P OP2 sing N N 119
U P "O5'" sing N N 120
U OP2 HOP2 sing N N 121
U "O5'" "C5'" sing N N 122
U "C5'" "C4'" sing N N 123
U "C5'" "H5'" sing N N 124
U "C5'" "H5''" sing N N 125
U "C4'" "O4'" sing N N 126
U "C4'" "C3'" sing N N 127
U "C4'" "H4'" sing N N 128
U "O4'" "C1'" sing N N 129
U "C3'" "O3'" sing N N 130
U "C3'" "C2'" sing N N 131
U "C3'" "H3'" sing N N 132
U "O3'" "HO3'" sing N N 133
U "C2'" "O2'" sing N N 134
U "C2'" "C1'" sing N N 135
U "C2'" "H2'" sing N N 136
U "O2'" "HO2'" sing N N 137
U "C1'" N1 sing N N 138
U "C1'" "H1'" sing N N 139
U N1 C2 sing N N 140
U N1 C6 sing N N 141
U C2 O2 doub N N 142
U C2 N3 sing N N 143
U N3 C4 sing N N 144
U N3 H3 sing N N 145
U C4 O4 doub N N 146
U C4 C5 sing N N 147
U C5 C6 doub N N 148
U C5 H5 sing N N 149
U C6 H6 sing N N 150
#
_em_ctf_correction.id 1
_em_ctf_correction.details 'CTF correction of 3D-maps by Wiener filtration'
_em_ctf_correction.type .
#
_em_image_processing.id 1
_em_image_processing.image_recording_id 1
_em_image_processing.details ?
#
_em_image_recording.details ?
_em_image_recording.id 1
_em_image_recording.avg_electron_dose_per_image 20
_em_image_recording.film_or_detector_model 'KODAK SO-163 FILM'
_em_image_recording.imaging_id 1
_em_image_recording.detector_mode ?
_em_image_recording.average_exposure_time ?
_em_image_recording.num_diffraction_images ?
_em_image_recording.num_grids_imaged ?
_em_image_recording.num_real_images ?
#
_em_specimen.experiment_id 1
_em_specimen.id 1
_em_specimen.concentration 32
_em_specimen.vitrification_applied YES
_em_specimen.staining_applied NO
_em_specimen.embedding_applied NO
_em_specimen.shadowing_applied NO
_em_specimen.details ?
#
loop_
_pdbx_coordinate_model.asym_id
_pdbx_coordinate_model.type
A 'P ATOMS ONLY'
B 'P ATOMS ONLY'
C 'P ATOMS ONLY'
#
loop_
_pdbx_initial_refinement_model.id
_pdbx_initial_refinement_model.type
_pdbx_initial_refinement_model.source_name
_pdbx_initial_refinement_model.accession_code
1 'experimental model' PDB 1KC9
2 'experimental model' PDB 1JFJ
#
_atom_sites.entry_id 1T1O
_atom_sites.fract_transf_matrix[1][1] 1.000000
_atom_sites.fract_transf_matrix[1][2] 0.000000
_atom_sites.fract_transf_matrix[1][3] 0.000000
_atom_sites.fract_transf_matrix[2][1] 0.000000
_atom_sites.fract_transf_matrix[2][2] 1.000000
_atom_sites.fract_transf_matrix[2][3] 0.000000
_atom_sites.fract_transf_matrix[3][1] 0.000000
_atom_sites.fract_transf_matrix[3][2] 0.000000
_atom_sites.fract_transf_matrix[3][3] 1.000000
_atom_sites.fract_transf_vector[1] 0.00000
_atom_sites.fract_transf_vector[2] 0.00000
_atom_sites.fract_transf_vector[3] 0.00000
#
_atom_type.symbol P
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM 1 P P . U A 1 1 ? -50.967 4.476 -88.756 1.00 88.72 ? 1061 U A P 1
ATOM 2 P P . G A 1 2 ? -50.803 8.850 -87.398 1.00 92.48 ? 1062 G A P 1
ATOM 3 P P . G A 1 3 ? -48.764 10.454 -81.417 1.00 90.30 ? 1063 G A P 1
ATOM 4 P P . C A 1 4 ? -46.814 8.130 -76.400 1.00 60.38 ? 1064 C A P 1
ATOM 5 P P . U A 1 5 ? -44.768 10.730 -72.531 1.00 100.31 ? 1065 U A P 1
ATOM 6 P P . U A 1 6 ? -42.193 15.381 -70.125 1.00 132.67 ? 1066 U A P 1
ATOM 7 P P . A A 1 7 ? -39.915 20.643 -71.603 1.00 134.62 ? 1067 A A P 1
ATOM 8 P P . G A 1 8 ? -40.942 19.987 -77.367 1.00 138.55 ? 1068 G A P 1
ATOM 9 P P . A A 1 9 ? -40.506 16.590 -81.730 1.00 132.45 ? 1069 A A P 1
ATOM 10 P P . A A 1 10 ? -38.713 10.950 -83.507 1.00 162.07 ? 1070 A A P 1
ATOM 11 P P . G A 1 11 ? -36.893 9.953 -90.206 1.00 112.73 ? 1071 G A P 1
ATOM 12 P P . C A 1 12 ? -32.645 9.139 -86.060 1.00 149.00 ? 1072 C A P 1
ATOM 13 P P . G B 2 1 ? -22.148 -0.316 5.233 1.00 67.41 ? 1906 G B P 1
ATOM 14 P P . G B 2 2 ? -22.343 -3.897 -0.839 1.00 72.07 ? 1907 G B P 1
ATOM 15 P P . C B 2 3 ? -24.417 -5.293 -4.807 1.00 89.20 ? 1908 C B P 1
ATOM 16 P P . C B 2 4 ? -29.004 -5.381 -8.824 1.00 103.74 ? 1909 C B P 1
ATOM 17 P P . G B 2 5 ? -34.694 -3.868 -9.953 1.00 105.00 ? 1910 G B P 1
ATOM 18 P P . U B 2 6 ? -38.362 -0.822 -11.879 1.00 161.61 ? 1911 U B P 1
ATOM 19 P P . A B 2 7 ? -37.723 4.926 -11.499 1.00 97.28 ? 1912 A B P 1
ATOM 20 P P . A B 2 8 ? -38.794 10.317 -14.640 1.00 117.57 ? 1913 A B P 1
ATOM 21 P P . C B 2 9 ? -36.866 14.500 -10.805 1.00 162.00 ? 1914 C B P 1
ATOM 22 P P . U B 2 10 ? -34.150 11.475 -14.990 1.00 27.21 ? 1915 U B P 1
ATOM 23 P P . A B 2 11 ? -29.304 8.162 -14.731 1.00 95.30 ? 1916 A B P 1
ATOM 24 P P . U B 2 12 ? -28.103 6.064 -9.146 1.00 84.23 ? 1917 U B P 1
ATOM 25 P P . A B 2 13 ? -29.985 4.223 -3.096 1.00 162.07 ? 1918 A B P 1
ATOM 26 P P . A B 2 14 ? -35.113 5.058 0.796 1.00 84.83 ? 1919 A B P 1
ATOM 27 P P . C B 2 15 ? -38.688 6.012 4.499 1.00 113.68 ? 1920 C B P 1
ATOM 28 P P . G B 2 16 ? -40.025 -0.476 6.468 1.00 107.14 ? 1921 G B P 1
ATOM 29 P P . G B 2 17 ? -39.847 -6.201 6.409 1.00 100.36 ? 1922 G B P 1
ATOM 30 P P . U B 2 18 ? -39.899 -12.137 7.084 1.00 135.00 ? 1923 U B P 1
ATOM 31 P P . C B 2 19 ? -34.477 -14.677 5.302 1.00 129.47 ? 1924 C B P 1
ATOM 32 P P . G C 3 1 ? -58.833 16.167 3.186 1.00 51.68 ? 1401 G C P 1
ATOM 33 P P . C C 3 2 ? -56.316 20.287 5.445 1.00 43.91 ? 1402 C C P 1
ATOM 34 P P . C C 3 3 ? -50.864 21.848 7.254 1.00 63.28 ? 1403 C C P 1
ATOM 35 P P . C C 3 4 ? -44.960 20.357 6.848 1.00 53.55 ? 1404 C C P 1
ATOM 36 P P . G C 3 5 ? -39.685 19.225 5.114 1.00 59.94 ? 1405 G C P 1
ATOM 37 P P . U C 3 6 ? -35.747 18.043 0.614 1.00 73.43 ? 1406 U C P 1
ATOM 38 P P . C C 3 7 ? -32.819 16.884 -4.002 1.00 76.27 ? 1407 C C P 1
ATOM 39 P P . A C 3 8 ? -33.387 18.644 -9.954 1.00 81.58 ? 1408 A C P 1
ATOM 40 P P . C C 3 9 ? -35.356 22.862 -13.317 1.00 86.68 ? 1409 C C P 1
ATOM 41 P P . A C 3 10 ? -36.463 28.221 -14.058 1.00 95.83 ? 1410 A C P 1
ATOM 42 P P . C C 3 11 ? -35.649 33.439 -12.106 1.00 163.78 ? 1411 C C P 1
ATOM 43 P P . C C 3 12 ? -33.015 37.408 -8.297 1.00 170.59 ? 1412 C C P 1
ATOM 44 P P . A C 3 13 ? -29.407 39.325 -4.185 1.00 107.44 ? 1413 A C P 1
ATOM 45 P P . U C 3 14 ? -24.617 38.585 -0.316 1.00 85.87 ? 1414 U C P 1
ATOM 46 P P . G C 3 15 ? -20.262 34.924 2.122 1.00 84.46 ? 1415 G C P 1
ATOM 47 P P . G C 3 16 ? -16.170 31.637 2.899 1.00 85.98 ? 1416 G C P 1
ATOM 48 P P . G C 3 17 ? -11.590 29.073 1.100 1.00 124.72 ? 1417 G C P 1
ATOM 49 P P . A C 3 18 ? -8.282 29.578 -4.086 1.00 150.89 ? 1418 A C P 1
ATOM 50 P P . G C 3 19 ? -3.657 29.502 -7.228 1.00 182.21 ? 1419 G C P 1
ATOM 51 P P . U C 3 20 ? -1.684 34.313 -10.649 1.00 149.75 ? 1420 U C P 1
ATOM 52 P P . A C 3 21 ? -14.928 43.207 -0.977 1.00 134.12 ? 1480 A C P 1
ATOM 53 P P . U C 3 22 ? -16.692 42.626 -6.504 1.00 133.09 ? 1481 U C P 1
ATOM 54 P P . G C 3 23 ? -17.539 39.084 -11.064 1.00 126.17 ? 1482 G C P 1
ATOM 55 P P . A C 3 24 ? -17.497 33.080 -12.431 1.00 131.52 ? 1483 A C P 1
ATOM 56 P P . C C 3 25 ? -18.247 27.992 -14.750 1.00 124.28 ? 1484 C C P 1
ATOM 57 P P . U C 3 26 ? -19.195 23.011 -11.445 1.00 116.70 ? 1485 U C P 1
ATOM 58 P P . G C 3 27 ? -21.920 21.033 -6.193 1.00 108.72 ? 1486 G C P 1
ATOM 59 P P . G C 3 28 ? -25.827 20.297 -2.231 1.00 119.99 ? 1487 G C P 1
ATOM 60 P P . G C 3 29 ? -30.602 22.542 1.944 1.00 73.32 ? 1488 G C P 1
ATOM 61 P P . G C 3 30 ? -34.380 26.081 4.120 1.00 89.26 ? 1489 G C P 1
ATOM 62 P P . U C 3 31 ? -39.079 29.637 4.421 1.00 139.41 ? 1490 U C P 1
ATOM 63 P P . G C 3 32 ? -43.409 31.805 1.491 1.00 184.39 ? 1491 G C P 1
ATOM 64 P P . A C 3 33 ? -47.355 31.636 -2.413 1.00 160.38 ? 1492 A C P 1
ATOM 65 P P . A C 3 34 ? -49.581 25.708 -5.275 1.00 200.93 ? 1493 A C P 1
ATOM 66 P P . G C 3 35 ? -50.203 21.115 -7.723 1.00 118.15 ? 1494 G C P 1
ATOM 67 P P . U C 3 36 ? -48.714 16.146 -10.216 1.00 79.93 ? 1495 U C P 1
ATOM 68 P P . C C 3 37 ? -46.807 11.263 -9.715 1.00 76.77 ? 1496 C C P 1
ATOM 69 P P . G C 3 38 ? -46.413 6.875 -6.579 1.00 65.71 ? 1497 G C P 1
ATOM 70 P P . U C 3 39 ? -46.959 4.896 -0.196 1.00 53.61 ? 1498 U C P 1
ATOM 71 P P . A C 3 40 ? -45.628 6.302 6.205 1.00 39.64 ? 1499 A C P 1
ATOM 72 P P . A C 3 41 ? -44.985 7.431 10.843 1.00 36.81 ? 1500 A C P 1
ATOM 73 P P . C C 3 42 ? -46.849 9.887 15.309 1.00 28.55 ? 1501 C C P 1
#