HEADER RNA 25-SEP-07 2Z9Q
TITLE TRANSFER RNA IN THE HYBRID P/E STATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRNA;
COMPND 3 CHAIN: A
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS;
SOURCE 3 ORGANISM_TAXID: 271
KEYWDS DISTORTED ANTICODON-STEM-LOOP, TWISTED CCA ARM, RNA
EXPDTA ELECTRON MICROSCOPY
MDLTYP P ATOMS ONLY, CHAIN A
AUTHOR J.FRANK,W.LI
REVDAT 6 13-MAR-24 2Z9Q 1 REMARK
REVDAT 5 11-DEC-19 2Z9Q 1 REMARK
REVDAT 4 13-JUL-11 2Z9Q 1 VERSN
REVDAT 3 14-APR-09 2Z9Q 1 REMARK
REVDAT 2 24-FEB-09 2Z9Q 1 VERSN
REVDAT 1 16-OCT-07 2Z9Q 0
JRNL AUTH W.LI,J.FRANK
JRNL TITL TRANSFER RNA IN THE HYBRID P/E STATE
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH M.VALLE,A.ZAVIALOV,J.SENGUPTA,U.RAWAT,M.EHRENBERG,J.FRANK
REMARK 1 TITL LOCKING AND UNLOCKING OF RIBOSOMAL MOTIONS
REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 114 123 2003
REMARK 1 REFN ISSN 0092-8674
REMARK 1 PMID 12859903
REMARK 1 DOI 10.1016/S0092-8674(03)00476-8
REMARK 2
REMARK 2 RESOLUTION. 11.70 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 SOFTWARE PACKAGES : SPIDER
REMARK 3 RECONSTRUCTION SCHEMA : NULL
REMARK 3
REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT
REMARK 3 PDB ENTRY : 1TTT
REMARK 3 REFINEMENT SPACE : REAL
REMARK 3 REFINEMENT PROTOCOL : OTHER
REMARK 3 REFINEMENT TARGET : CROSS CORRELATION COEFFICIENT
REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL
REMARK 3
REMARK 3 FITTING PROCEDURE : REFINEMENT PROTOCOL--AUTO
REMARK 3
REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS
REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 2.800
REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL
REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 11.70
REMARK 3 NUMBER OF PARTICLES : NULL
REMARK 3 CTF CORRECTION METHOD : NULL
REMARK 3
REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV
REMARK 3
REMARK 3 OTHER DETAILS: THE STRUCTURE CONTAINS P ATOMS ONLY
REMARK 4
REMARK 4 2Z9Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ.
REMARK 100 THE DEPOSITION ID IS D_1000027698.
REMARK 245
REMARK 245 EXPERIMENTAL DETAILS
REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE
REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM)
REMARK 245
REMARK 245 ELECTRON MICROSCOPE SAMPLE
REMARK 245 SAMPLE TYPE : PARTICLE
REMARK 245 PARTICLE TYPE : POINT
REMARK 245 NAME OF SAMPLE : EF-G BOUND RELEASE COMPLEX IN
REMARK 245 THE PRESENCE OF PUROMYCIN AND
REMARK 245 GDPNP
REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 32.00
REMARK 245 SAMPLE SUPPORT DETAILS : CARBON ON QUANTIFOIL GRIDS
REMARK 245 SAMPLE VITRIFICATION DETAILS : PLUNGED INTO ETHANE
REMARK 245 SAMPLE BUFFER : POLYMIX
REMARK 245 PH : 7.50
REMARK 245 SAMPLE DETAILS : NULL
REMARK 245
REMARK 245 DATA ACQUISITION
REMARK 245 DATE OF EXPERIMENT : 01-JUN-01
REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL
REMARK 245 TEMPERATURE (KELVIN) : 80.00
REMARK 245 MICROSCOPE MODEL : FEI TECNAI F20
REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM
REMARK 245 MINIMUM DEFOCUS (NM) : 1.75
REMARK 245 MAXIMUM DEFOCUS (NM) : 3.93
REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00
REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00
REMARK 245 NOMINAL CS : 2.00
REMARK 245 IMAGING MODE : BRIGHT FIELD
REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 1500.00
REMARK 245 ILLUMINATION MODE : FLOOD BEAM
REMARK 245 NOMINAL MAGNIFICATION : 50000
REMARK 245 CALIBRATED MAGNIFICATION : 49696
REMARK 245 SOURCE : FIELD EMISSION GUN
REMARK 245 ACCELERATION VOLTAGE (KV) : 200
REMARK 245 IMAGING DETAILS : SAMPLES WERE MAINTAINED AT
REMARK 245 LIQUID NITROGEN
REMARK 247
REMARK 247 ELECTRON MICROSCOPY
REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON
REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE
REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES
REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION
REMARK 247 OF THE STRUCTURE FACTORS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1TTT RELATED DB: PDB
REMARK 900 COORDINATES FOR STARTING THE MD SIMULATION
REMARK 900 RELATED ID: 1PN6 RELATED DB: PDB
REMARK 900 COORDINATES OF FITTING STRUCTURE OF EF-G AS A REFERENCE POSITION
REMARK 900 FOR THE P/E-TRNA.
REMARK 900 RELATED ID: EMD-1363 RELATED DB: EMDB
DBREF 2Z9Q A 1 75 PDB 2Z9Q 2Z9Q 1 75
SEQRES 1 A 75 C G G A U U U A 2MG C U C A
SEQRES 2 A 75 G H2U H2U G G G A G A G C M2G C
SEQRES 3 A 75 C A G A OMC U OMG A A YYG A PSU 5MC
SEQRES 4 A 75 U G G A G 7MG U C 5MC U G U G
SEQRES 5 A 75 5MU PSU C G 1MA U C C A C A G A
SEQRES 6 A 75 A U U C G C A C C A
MODRES 2Z9Q 2MG A 9 G 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
MODRES 2Z9Q H2U A 15 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
MODRES 2Z9Q H2U A 16 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
MODRES 2Z9Q M2G A 25 G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
MODRES 2Z9Q OMC A 31 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
MODRES 2Z9Q OMG A 33 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
MODRES 2Z9Q YYG A 36 G
MODRES 2Z9Q PSU A 38 U PSEUDOURIDINE-5'-MONOPHOSPHATE
MODRES 2Z9Q 5MC A 39 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE
MODRES 2Z9Q 7MG A 45 G
MODRES 2Z9Q 5MC A 48 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE
MODRES 2Z9Q 5MU A 53 U 5-METHYLURIDINE 5'-MONOPHOSPHATE
MODRES 2Z9Q PSU A 54 U PSEUDOURIDINE-5'-MONOPHOSPHATE
MODRES 2Z9Q 1MA A 57 A
HET 2MG A 9 1
HET H2U A 15 1
HET H2U A 16 1
HET M2G A 25 1
HET OMC A 31 1
HET OMG A 33 1
HET YYG A 36 1
HET PSU A 38 1
HET 5MC A 39 1
HET 7MG A 45 1
HET 5MC A 48 1
HET 5MU A 53 1
HET PSU A 54 1
HET 1MA A 57 1
HETNAM 2MG 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
HETNAM H2U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
HETNAM M2G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
HETNAM OMG O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
HETNAM YYG 4-(3-[5-O-PHOSPHONORIBOFURANOSYL]-4,6-DIMETHYL-8-OXO-4,
HETNAM 2 YYG 8-DIHYDRO-3H-1,3,4,5,7A-PENTAAZA-S-INDACEN-YLAMINO-
HETNAM 3 YYG BUTYRIC ACID METHYL ESTER
HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE
HETNAM 5MC 5-METHYLCYTIDINE-5'-MONOPHOSPHATE
HETNAM 7MG 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE
HETNAM 5MU 5-METHYLURIDINE 5'-MONOPHOSPHATE
HETNAM 1MA 6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
HETSYN YYG MODIFIED GUANOSINE-5'-PHOSPHATE
FORMUL 1 2MG C11 H16 N5 O8 P
FORMUL 1 H2U 2(C9 H15 N2 O9 P)
FORMUL 1 M2G C12 H18 N5 O8 P
FORMUL 1 OMC C10 H16 N3 O8 P
FORMUL 1 OMG C11 H16 N5 O8 P
FORMUL 1 YYG C21 H29 N6 O12 P
FORMUL 1 PSU 2(C9 H13 N2 O9 P)
FORMUL 1 5MC 2(C10 H16 N3 O8 P)
FORMUL 1 7MG C11 H18 N5 O8 P
FORMUL 1 5MU C10 H15 N2 O9 P
FORMUL 1 1MA C11 H16 N5 O7 P
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
ATOM 1 P C A 1 -14.930 -53.123 25.540 1.00 10.00 P
ATOM 2 P G A 2 -19.319 -50.341 29.207 1.00 10.00 P
ATOM 3 P G A 3 -24.194 -45.226 30.319 1.00 10.00 P
ATOM 4 P A A 4 -27.637 -40.442 30.702 1.00 10.00 P
ATOM 5 P U A 5 -31.420 -36.117 28.621 1.00 10.00 P
ATOM 6 P U A 6 -35.287 -35.045 24.391 1.00 10.00 P
ATOM 7 P U A 7 -38.095 -33.869 18.380 1.00 10.00 P
ATOM 8 P A A 8 -43.421 -32.141 17.878 1.00 10.00 P
HETATM 9 P 2MG A 9 -46.229 -30.855 12.830 1.00 10.00 P
ATOM 10 P C A 10 -40.050 -28.350 11.818 1.00 10.00 P
ATOM 11 P U A 11 -36.941 -25.027 16.534 1.00 10.00 P
ATOM 12 P C A 12 -35.673 -23.240 21.825 1.00 10.00 P
ATOM 13 P A A 13 -37.970 -26.575 27.583 1.00 10.00 P
ATOM 14 P G A 14 -40.063 -27.830 32.245 1.00 10.00 P
HETATM 15 P H2U A 15 -40.464 -33.744 34.043 1.00 10.00 P
HETATM 16 P H2U A 16 -40.488 -39.811 35.485 1.00 10.00 P
ATOM 17 P G A 17 -45.751 -44.639 36.005 1.00 10.00 P
ATOM 18 P G A 18 -50.821 -43.712 33.795 1.00 10.00 P
ATOM 19 P G A 19 -56.236 -41.471 30.677 1.00 10.00 P
ATOM 20 P A A 20 -54.385 -38.683 26.557 1.00 10.00 P
ATOM 21 P G A 21 -54.105 -32.759 26.449 1.00 10.00 P
ATOM 22 P A A 22 -53.470 -26.925 27.564 1.00 10.00 P
ATOM 23 P G A 23 -51.760 -20.204 25.213 1.00 10.00 P
ATOM 24 P C A 24 -48.590 -15.284 21.299 1.00 10.00 P
HETATM 25 P M2G A 25 -47.419 -14.164 15.590 1.00 10.00 P
ATOM 26 P C A 26 -48.696 -15.537 9.963 1.00 10.00 P
ATOM 27 P C A 27 -52.726 -16.621 6.762 1.00 10.00 P
ATOM 28 P A A 28 -58.394 -16.393 5.398 1.00 10.00 P
ATOM 29 P G A 29 -63.860 -14.237 7.157 1.00 10.00 P
ATOM 30 P A A 30 -67.473 -10.822 10.680 1.00 10.00 P
HETATM 31 P OMC A 31 -69.254 -7.393 15.934 1.00 10.00 P
ATOM 32 P U A 32 -66.784 -2.724 18.589 1.00 10.00 P
HETATM 33 P OMG A 33 -65.655 2.329 16.532 1.00 10.00 P
ATOM 34 P A A 34 -63.503 0.509 12.001 1.00 10.00 P
ATOM 35 P A A 35 -58.320 -2.911 10.626 1.00 10.00 P
HETATM 36 P YYG A 36 -53.522 -5.830 13.079 1.00 10.00 P
ATOM 37 P A A 37 -50.595 -7.374 18.299 1.00 10.00 P
HETATM 38 P PSU A 38 -52.660 -9.922 23.441 1.00 10.00 P
HETATM 39 P 5MC A 39 -57.137 -14.463 24.748 1.00 10.00 P
ATOM 40 P U A 40 -62.174 -18.626 24.198 1.00 10.00 P
ATOM 41 P G A 41 -64.634 -22.295 20.929 1.00 10.00 P
ATOM 42 P G A 42 -63.840 -26.157 16.363 1.00 10.00 P
ATOM 43 P A A 43 -61.886 -29.153 12.431 1.00 10.00 P
ATOM 44 P G A 44 -56.424 -31.686 12.493 1.00 10.00 P
HETATM 45 P 7MG A 45 -51.298 -33.556 12.124 1.00 10.00 P
ATOM 46 P U A 46 -49.177 -38.400 13.609 1.00 10.00 P
ATOM 47 P C A 47 -46.352 -41.484 19.444 1.00 10.00 P
HETATM 48 P 5MC A 48 -40.293 -39.224 20.698 1.00 10.00 P
ATOM 49 P U A 49 -41.961 -42.797 15.493 1.00 10.00 P
ATOM 50 P G A 50 -42.120 -47.777 12.947 1.00 10.00 P
ATOM 51 P U A 51 -43.427 -53.100 13.162 1.00 10.00 P
ATOM 52 P G A 52 -45.080 -57.913 17.112 1.00 10.00 P
HETATM 53 P 5MU A 53 -45.931 -60.347 23.701 1.00 10.00 P
HETATM 54 P PSU A 54 -47.889 -60.481 28.748 1.00 10.00 P
ATOM 55 P C A 55 -52.694 -59.383 31.692 1.00 10.00 P
ATOM 56 P G A 56 -54.393 -56.212 27.295 1.00 10.00 P
HETATM 57 P 1MA A 57 -52.381 -50.885 25.266 1.00 10.00 P
ATOM 58 P U A 58 -49.697 -44.986 24.395 1.00 10.00 P
ATOM 59 P C A 59 -44.254 -46.142 24.910 1.00 10.00 P
ATOM 60 P C A 60 -39.896 -45.466 30.136 1.00 10.00 P
ATOM 61 P A A 61 -37.053 -50.103 30.057 1.00 10.00 P
ATOM 62 P C A 62 -33.584 -54.299 27.868 1.00 10.00 P
ATOM 63 P A A 63 -30.363 -55.942 23.445 1.00 10.00 P
ATOM 64 P G A 64 -28.415 -52.859 18.219 1.00 10.00 P
ATOM 65 P A A 65 -27.745 -48.674 13.367 1.00 10.00 P
ATOM 66 P A A 66 -27.530 -43.841 10.361 1.00 10.00 P
ATOM 67 P U A 67 -25.273 -38.405 12.757 1.00 10.00 P
ATOM 68 P U A 68 -23.126 -33.790 15.369 1.00 10.00 P
ATOM 69 P C A 69 -20.122 -32.125 20.123 1.00 10.00 P
ATOM 70 P G A 70 -16.278 -33.268 23.855 1.00 10.00 P
ATOM 71 P C A 71 -11.710 -35.792 27.674 1.00 10.00 P
ATOM 72 P A A 72 -7.487 -40.169 29.988 1.00 10.00 P
ATOM 73 P C A 73 -4.198 -45.249 27.918 1.00 10.00 P
ATOM 74 P C A 74 -3.111 -49.932 22.688 1.00 10.00 P
ATOM 75 P A A 75 3.778 -48.307 20.830 1.00 10.00 P
TER 76 A A 75
MASTER 111 0 14 0 0 0 0 6 75 1 0 6
END