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6IR9

Rna polymerase ii elongation complex bound with elf1 and spt4/5, stalled at shl(-1) of the nucleosome

PDB DOI: 10.2210/pdb6ir9/pdb

Classification: TRANSCRIPTION/RNA/DNA
Organism(s): Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct

Deposited: 2018-11-12
Deposition Author(s): Ehara, H. , Fujino, Y. , Kujirai, T. , Kurumizaka, H. , Sekine, S. , Shirouzu, M.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.8 Å

6ir9
Literature

Rna polymerase ii elongation complex bound with elf1 and spt4/5, stalled at shl(-1) of the nucleosome

Ehara, H. , Fujino, Y. , Kujirai, T. , Kurumizaka, H. , Sekine, S. , Shirouzu, M.

Primary Citation of Related Structures: 6IR9


Proteins
Molecule Chains Sequence Length Organism Sequence
Histone H3.3 A 139 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III J 72 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct MIIPVRCFSCGKVVGDKWDAYLRLLEEGKQEGDALDELKLKRYCCRRMVLTHVDLIEKFLRYNPLEKKDFDS
RNA polymerase II subunit B12.5 K 118 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct MNAPDRFELFILPDDVPKLKITPDSRVPNCIIIKFEREDHTLANLLREELALYPDVTFVAYKVEHPLFANFVMRLQTEEGTRPKQALERACASIINKLKTLDHKFNEEWNIKNFSLND
RNA polymerase subunit ABC10-alpha L 72 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct MSREGFVAPSGTDLAAAASGVAPNKHYGVKYTCGACAHNFSLNKSDPVRCKECGHRVIYKARTKRMIQFDAR
Transcription elongation factor 1 homolog M 113 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct GPGMGKRKSSARKPAPKIKQKLETQFTCLFCNHDNSVVCTLDKKNSIGLLECKKCNLSFQAPINSLSQPIDIYSDWIDACEAVAEENADVNGDNFIENDGADREQDDDYDDEF
Transcription elongation factor SPT4 V 108 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct MRERACMLCGIVLPGRVFMQNGCPNCDSVLNLRDSDQATVNECTSSSFEGLVAVGDNEHSWVAKWLRVDRFQPGLYAVRVDGRLPSDIVAALEQYGVYYRPRDGSVID
Spt5 W 911 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct GPGMSETHKNQLDKVSTVSPDGPSEAVKEHSLQSKDLSKNDGQFIVPLDRNVIEQEEHKQVKSSAQAHNTTGDAADNEIEDGVPSEDVEFDKFKEDDYDEDDEVEEEGDIRSRKRRRHNQFLDVEAEVDDEEDDDDDDDDVELKHDFIQDDHIQHETQNEGFIAGHVDDDRLHRKLDQSREKIADQDAQELADEFKQRYGRSASSKYMGSASTTAPQRLLIPTVDDPGIWGVKVRLGKEKDVVRQILKKKLAREGTKNPLEIYSAFQRDSFKGHVYIEARKAEAINDALKGNVNVFSNNSKFLVGIVEYKDLLRPVKSSDVKLTRGSYVRVKNGKFKGDLAQVDEVLENGLEARLKLVPRLDYGKDLSHLSTSSSVDSTKNRRKFYTSKFRPAQRLFSEAEARVHEPTIRRDRDGFVTYGGEEYYEGFLYKTFRLQNLIVNSINPTLNELSLFQSNEESTTIDLSTIADSLKETAKNLVSFQPGDNVEIINGELNHLTGTVSSVNQSTIVSVRLHSDDDTINSETVEIPTSDLRKIFNVGDHVRVIHGKHTDDTGLIVEVNGDKVEFISNQTKRTVIVFSNYLIKSTDSTVSINESGRFELHDLVQVNSDLVGIVIRAQKDSFDVLCSDGKLLSLPPVSIYSKLNLNPNQQIAIDSNGVEVKVGDTVREFTGERRQGTILHVYRNFLFLRSREIVENQGVFVTSSNRVKTITSKSNGTGGQISGPDLSRMNPSRVIPPPSIPVANQRMTGRDPTLNKTVKIRQGGYKGKIGIVKEANGDRFRVELHNPNKTIPIPCSFLLIESTHGWVPYEDFVASDRRGGNIPRHEISGHVQQPQHGRAPAWGSGGKTPAWGSGGKTPAWGSGGSGGKTPAWGSGGKTPTWGSGAKTPAWGSGSKTPAWSGLDEEDRRDF
RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III E 214 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct MEDNNRIISRLWRSFRTVKEMAADRGYFISQEEMDQSLEEFRSKICDSMGNPQRKLMSFLANPTPEALEKYSDLGTLWVEFCDEPSVGIKTMRNFCLRIQEKNFSTGIFIYQNNITPSANKMIPTVSPAIIETFQESDLVVNITHHELVPKHIRLSDGEKSQLLQRYKLKESQLPRIQREDPVARYLGLKRGQVVKIIRRSETSGRYASYRICL
Histone H4 B 106 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III F 155 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct MSEDEAFNEQTENFENFEDEHFSDDNFEDRSTQPEDYAVGVTADGRQIINGDGIQEVNGTIKAHRKRSNKELAILKEERTTTPYLTKYERARILGTRALQISMNAPVLVDIEGETDPLQIAMKELSQRKIPLVIRRYLPDGSYEDWGCDELIVDN
RNA polymerase II third largest subunit B44, part of central core C 304 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct MSKEPKVNIINAQDDEVELMLSDVNLSLANSLRRTMLAEVPTLAIDLVEIKMNTSVLADEFISHRLGLIPLVSEDVEEMKYSRDCTCEDYCDECSVVLELSARHEGEEGTTDVYSSSLIKVSGPGNLNVGEPVRRDDYDQGILLCKLRNHQELNIRCIAKKGIAKEHAKWSPCSAIAFEYDPHNKLKHTDFWFEVDAKKEWPDSKYATWEEPPKPGEVFDYKAKPNRFYMTVETTGSLKANQVFSRGIKTLQEKLANVLFELENSRPANTTAYGGATAYGGQTVYGRETSYGGNTNYGDYNAPY
RNA polymerase II subunit G 171 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct MFFLKDLSLILTLHPSYFGPQMNQYLREKLLTDVEGTCTGQFGYIVTVLDGMNIDVGKGRIIPGSGSAEFEVKYRAVVWKPFKGEVVDAIVSNVSPIGFFADVGPLNVFVSTRLIPDNLVYNPSNSPPAYMSNDELITKGSKVRLKVVGTRTDVNEIYAIGSIKEDFLGAI
RNA polymerase II subunit B32 D 186 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct MNVSTSTVGARRRRAKQQVDDEENATLLRLGPEFALKQYDHDGNEHDLIALSLSESRLLIREALKARSRARNGGVDIESSNGEIDDDELAKVTSGAVANGVVKKTLDYLNTFARFKDEETCTAVDQLLHNSSDCSVLHPFEIAQLSSLGCEDVDEAITLIPSLAAKKEVNLQRILDELNRLEDPYK
DNA-directed RNA polymerases I, II, and III subunit RPABC3 H 145 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct MSSALFDDIFTVQTVDNGRYNKVSRIIGISTTNSAIKLTLDINNEMFPVSQDDSLTVTLANSLSLDGEDESANFSKSWRPPKPTDKSLADDYDYVMFGTVYKFEEGDEDKIKVYVSFGGLLMCLEGGYKSLASLKQDNLYILIRR
DNA-directed RNA polymerase subunit I 115 Homo Sapiens , Komagataella Phaffii , Komagataella Phaffii (Strain Atcc 76273 / Cbs 7435 / Cect 11047 / Nrrl Y-11430 / Wegner 21-1) , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct MASFRFCLECNNMLYPKEDKENQRLLYSCRNCDYTELAEDPKVYRHELITNIGETAGIVDDIGQDPTLPRSDKECPECHSRDCVFFQSQQRRKDTNMTLFYVCLNCKKTFRDESE

Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
RNA (5'-R(P*GP*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*U)-3') p 16 NA GCCUGGUGUCUUGGGU
DNA (198-MER) t 198 NA ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACACCCAAGACACCAGGCACGAGACAGAAAAAAACAACGAAAACGGCCACCACCCAAACACACCAAACACAAGAGCTAATTGACTGACGTAAGC
DNA (198-MER) n 198 NA GCTTACGTCAGTCTGGCCATCTTTGTGTTTGGTGTGTTTGGGTGGTGGCCGTTTTCGTTGTTTTTTTCTGTCTCGTGCCTGGTGTCTTGGGTGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGAT
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2018-11-12
Deposition Author(s): Ehara, H. , Fujino, Y. , Kujirai, T. , Kurumizaka, H. , Sekine, S. , Shirouzu, M.