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FASTA Sequence PDB Format mmCIF Format
FASTA Sequence PDB Format PDB Format(gz) PDBx/mmCIF Format PDBx/mmCIF Format(gz) PDBML/XML Format Validation Full PDF Validation CIF

7XSZ

Rna polymerase ii elongation complex transcribing a nucleosome (ec115)

PDB DOI: 10.2210/pdb7xsz/pdb

Classification: TRANSCRIPTION
Organism(s): Homo Sapiens , Komagataella Phaffii , Synthetic Construct

Deposited: 2022-05-15
Deposition Author(s): Ehara, H. , Kujirai, T. , Kurumizaka, H. , Sekine, S. , Shirouzu, M.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.4 Å

7xsz
Literature

Rna polymerase ii elongation complex transcribing a nucleosome (ec115)

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

Primary Citation of Related Structures: 7XSZ


Proteins
Molecule Chains Sequence Length Organism Sequence
Histone H3.3 A 139 Homo Sapiens , Komagataella Phaffii , Synthetic Construct GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III J 72 Homo Sapiens , Komagataella Phaffii , Synthetic Construct MIIPVRCFSCGKVVGDKWDAYLRLLEEGKQEGDALDELKLKRYCCRRMVLTHVDLIEKFLRYNPLEKKDFDS
RNA polymerase II subunit B12.5 K 118 Homo Sapiens , Komagataella Phaffii , Synthetic Construct MNAPDRFELFILPDDVPKLKITPDSRVPNCIIIKFEREDHTLANLLREELALYPDVTFVAYKVEHPLFANFVMRLQTEEGTRPKQALERACASIINKLKTLDHKFNEEWNIKNFSLND
RNA polymerase subunit ABC10-alpha L 72 Homo Sapiens , Komagataella Phaffii , Synthetic Construct MSREGFVAPSGTDLAAAASGVAPNKHYGVKYTCGACAHNFSLNKSDPVRCKECGHRVIYKARTKRMIQFDAR
Transcription elongation factor Spt6 M 1503 Homo Sapiens , Komagataella Phaffii , Synthetic Construct GPGMSAPSPSVSEEDINETRNSIDADASTVQDLLDQDAQEGSGSDNEGSNIVDSSEEDDDEDDEEEMQKVREGFIVDDDDENDEDGIPSSTKRKHRKKHKKRSAEVVEEVDEDDLQLLMENSGAVPGQQQNVKFKRLKRAEQDEKAQDSDSRGLNDMFSDEEGPGGVVEEGSEEEGLEDNLTTKTQRSGNLPHDEFDDFIEEDEFSDEDDEARDERLARMRSAKAAPQLAGLQGEQYQEIIEIFGDGTDYQWTLDAEEEMEQPQQDQEYDEAGEEIKGTTTSLADVFEPSELKEKMLTDEDNVIRVTDLPERFQAYRKSIKNYKLSDVDYSNERDWIVEQLKLEKRDFLQHLTQAHSSVAHLEEKFEASVKKIVDFIAIESFEVPFIWNHRRDYALHTYNDDSNNTIIVKLLNEDDLWRIVQLDLDYHSIHDKKAALSSIYKQLDLDVVDPTYEEFFGSARTLSELQDIDDYLTFNYSSQVKNLTAVAELSIEGNGSGEDEEQTTKSSFAEVKMKRKYSKYAIYDRIRQDAIYPVVQSIANISQMRENLAQSKRLHQVEDPIESPMDMIADIMSTEKDKTTFISSEKAYQAVKQFFSEQLSYEPFIRKTIRTAFQSFGVINIELTERGKLQIEPESPYFDFKYAKNRPISALTATPDLYLRMIQAENDGLVNIKVELPMLSTVVDHFYNILKSDGTSEISEKWNALRNDAWKQSLDKLIPLVQLNVKESIRRDCERVLYFQVKNSFTKKIDQAPYQPPTYAKGTIPRVLTLSFGEGNRGDAVLGVFMDDSGDVKSQIKFDEDFQSRDFSDSLTRYIKSNNINPDIIGISGFNIHTKKLFDKVNELVNEERLTIEYDNEYGYDREEDGRSDKHLIRVIYVNDETARLYQHSSKSSAEYPNRPQLAKYCIGLAKYIQSPLLEYLALDESMYSLHIHKHQNLLPREKLIDAVQTSIVDIVNLVGVDINEAVRAPYHALALPYVCGLGPRKAAGLIQSIQRIGSNLVNRAHLITEQLTSKTVFLNMASFVYIVFDPDVERNPQGEMDLLDSTRIHPEDYSLARKMAADALDIEDIDDDDESAMRNAIYEMVFPRSPPKDEDDLTFKLDELILDDYATELERKHQLKKRSTLQIIKEELQSRYREIRRDFHILNEAEIFQLLTRETVDSFRKGMVIPVYVRKVESSYMSVSTQSLIAGNIQRQDILEPNDRRDPREVYSVGQTVRACILDVDYYNFKCQLSLLRQFTENQVAGLNVNRNPKFWDIESENRDRQEEIDKQREESRESRVIKHPFFHNMKSKEAEDYLAARPVGDVVIRPSSKGSNHITISWKVAPQLYQHIDVLEENKDDANAIGRVLLVGKYRYHDLDELLVEYVNNVANKVELMVSHDKFMSDSLDYVKEWLERYSKANGNRSHYIFTFNRKAPGWFFLLFKLNPTSEIKIWNVKALPDGYLLANNVYPDTNSLCNGFKTLMSSRRQIKQRSNRAGGEYNNSHAGAYDNGYSNAPRY
Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II N 417 Homo Sapiens , Komagataella Phaffii , Synthetic Construct GPGMSDEESENKKLLDQVLPEKTDQETQPEADAALAEQEAPENEPNEPASDDDSDSDLSDISDVDEEKVAEGLRYLDEQTAASLSKHKAAQPSSTHKKKEPTRRRPKQQTARETQYEPDVVEDEAARRTRLFEEKLDAAIKRKPNKRKKNDDVDLEQMQDELIQQLKLQMEESAIRDANNIEQGKPAIFKLKLLPKVKDILLRANLADSILDNNLLASVRLWLEPLPDASLPAYQIQKVLFDAIKSLPIKTSHLRESGLGKVMVFYQKSKRVEPNLKRTAEKLISDWTRPIMGASDNYKDMRVRTQQFDPAQFAESLPGRVSVRPQEAKTLYEEAAERRKRAAIPQARTAAYTIAPQVNTELLMSSARRTLPSGVGSSLSGEDQYKRLNSRLNTMGTKRKSSAKKGGISIEGRGLPQ
RNAP II-associated protein V 396 Homo Sapiens , Komagataella Phaffii , Synthetic Construct GSAMTSSKSRQDYIAKVRYQNDLPAPPCPPKLLKYEIEKEAPQKEFLKDSRLLSALFSKDNFRYLMNETSDGLDVNYLRIPGIIENEKSLGKLFSSYKNLAIENLHPDDRLLLVDPNKSATLNEESPVFFLRRPQYVSDGEKINLQNFTNKRKHQDMEDTNPRSQLHSVERTFDEVIDPRNKNRLQSLIHPRKKIKAVKAWHFFPDTSTFDQVFHSLKFVGSASLSKDRPLNEQLGQVSETDSTSVNASILTSLFKPIEINPHNKWISLYAVTDKLSAESFRKSFNSIKDDNIVNRHVIYDHIKDFDQMFRGHKKLFEDFAISFDDISDRAFFVPIVGRLELKKKRIVPGLVDMVNRTNYAHIRMDLRNPSTQETAIRDSRREQYDPVNYSSIQEE
Transcription elongation factor SPT5 W 911 Homo Sapiens , Komagataella Phaffii , Synthetic Construct GPGMSETHKNQLDKVSTVSPDGPSEAVKEHSLQSKDLSKNDGQFIVPLDRNVIEQEEHKQVKSSAQAHNTTGDAADNEIEDGVPSEDVEFDKFKEDDYDEDDEVEEEGDIRSRKRRRHNQFLDVEAEVDDEEDDDDDDDDVELKHDFIQDDHIQHETQNEGFIAGHVDDDRLHRKLDQSREKIADQDAQELADEFKQRYGRSASSKYMGSASTTAPQRLLIPTVDDPGIWGVKVRLGKEKDVVRQILKKKLAREGTKNPLEIYSAFQRDSFKGHVYIEARKAEAINDALKGNVNVFSNNSKFLVGIVEYKDLLRPVKSSDVKLTRGSYVRVKNGKFKGDLAQVDEVLENGLEARLKLVPRLDYGKDLSHLSTSSSVDSTKNRRKFYTSKFRPAQRLFSEAEARVHEPTIRRDRDGFVTYGGEEYYEGFLYKTFRLQNLIVNSINPTLNELSLFQSNEESTTIDLSTIADSLKETAKNLVSFQPGDNVEIINGELNHLTGTVSSVNQSTIVSVRLHSDDDTINSETVEIPTSDLRKIFNVGDHVRVIHGKHTDDTGLIVEVNGDKVEFISNQTKRTVIVFSNYLIKSTDSTVSINESGRFELHDLVQVNSDLVGIVIRAQKDSFDVLCSDGKLLSLPPVSIYSKLNLNPNQQIAIDSNGVEVKVGDTVREFTGERRQGTILHVYRNFLFLRSREIVENQGVFVTSSNRVKTITSKSNGTGGQISGPDLSRMNPSRVIPPPSIPVANQRMTGRDPTLNKTVKIRQGGYKGKIGIVKEANGDRFRVELHNPNKTIPIPCSFLLIESTHGWVPYEDFVASDRRGGNIPRHEISGHVQQPQHGRAPAWGSGGKTPAWGSGGKTPAWGSGGSGGKTPAWGSGGKTPTWGSGAKTPAWGSGSKTPAWSGLDEEDRRDF
Histone H4 B 106 Homo Sapiens , Komagataella Phaffii , Synthetic Construct GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Component of the Paf1p complex Q 1084 Homo Sapiens , Komagataella Phaffii , Synthetic Construct MKDHLIHNHHKHEHAHAEHDYKDDDDKEHLYFQGSSGSSGMSLLDQDYYLSALPEDKRAELVTLQLTIPLKSGDEVVTIDFNEDVDVSQLCVLLESENARPDLWLSAAKVFVSKGNIAGSQEIIRKALQSNVILDSSASVTSLFHNFSFWLSLMEYVSTNSREDQFLEYASNSLQASNSLDSGLILNGIGNGVLYAKSRRYDEALKEFDNLLKKKSTNILAILGKAQILYKRQKYSQALELYQKALTINPLIVPDPRLGIGLCFWHLNNKQLAEQAWHNSLKVHPQNNLNTKILICLAKFDYCFNESKDDDEFTALYRESLEFLHSCLKEDAKHPLLLMVLASYYFSKEDYEKVEKLCNLVLKENSRNAAFVSASHFWLARVAYHKEDYVQAQKQFKQAEDSQNSNTLAKLGYAQCLIARNEVGDATIYLEKFFKENQDSKSSEMMLLLGIIYSQSGKSYYKAIIFLEKYVAVCQEENYPILPEAYLVLSRVYENKDLNVALDYLMKANDILGDKANVYVLNNLGIYHFFRNNVSQSSDFFAQSLEALNNVSPQNKEALSITLHYNKARVEEVSNQSEAEKLYSKLMEKCPGYTSNKIRYIYLLALKSNGNNYADVQQLLDDFPSDLEVRSFYGWFLKRYGRKNGLKQDLESQHHKDTLINYDKHDCYALLSLGNIYATIAREMKVTDQKQNEIKRQQYLRAAQFYHKVLSIDPKNIYAAQGIAIIFSDKERTGLALEIFKKVRDTVQDLGTFINLGHCFMEAKQFGKAIESYTIALEKFSNGMDSKLLVLIGRAWYHRGFYEKSMDAYKKALEVSEQAYQLSKLPALRFNIVFIQFQIADFVKSLPNTQRDLTTLENALSGLNDAIKSLLKLAELEQPPYPSEDLKARATMGSNTLRNQLERAIQDQQDYEMSIQEKLRTARRKQQLDEEKRLEQEQRRLEEARKRQEAELIKRQELIKQAEEWNKMDIDAAKDNNDVLSEDGGEGEKKTTKKRKRKQKVSEDIAPDLDRINEENGNTEDYDPILDNEEEENYDEKDSENKENGQNGQNEEVYPESEGDDEDDVTNTKRQKRSKGIVDEEDSE
RNAPII-associated chromatin remodeling Paf1 complex subunit R 544 Homo Sapiens , Komagataella Phaffii , Synthetic Construct MKDHLIHNHHKHEHAHAEHLYFQGSSGSSGMSDKEQDLDEDLLALAGAGSDSESNSAYSPEQEVSRKSKKIVNDSEDENNDSDGEQLLNPYPLEDKFKDEADRARLLGLSEMEREAILYERSQEVIKLKEKHLLSLRAKQSQLEKTAREGPKSSKTNKLSELKKQREQKSKRQRSDEYSDEEDDYRYEEVGDNDDVEMSDNYIDEDDAVFVEPKKSSRSQELSKPATLSDINKIIFGRTAMSKYWYYPEFDDVVKGMYLRLNTGSGGNGFSPYKVVEVLGSQRIKGSAYGLNSKENNCDMYLKVAFPNQKEMVRPLFVFSDSSITHPEFDLFLRELDAEGLSVMDLRDVDYKYHQLKEMSSRSLSNDEVNSIVKMKQSLSSNTGFNTVLKKAQLQEELEEARDAHDHERVARIEAELKSIGAESVVASKASSSMLKIDQRNKKLNNRFIRKAEMAAVEKRKLRGTSESDPFYRLATTARMFYKSANLGADDSNQPKTKAELEEEAKQEKKLEMQKLESMVKSNYRNGGLDRIISKIDFDFDLEL
Leo1 U 459 Homo Sapiens , Komagataella Phaffii , Synthetic Construct MKDHLIHNHHKHEHAHAEHLYFQGSSGSSGMSQELEQNRHSGEESPDPVLDANTSDVDDDGLDLFGDDDDEQPEAKPGQLDDSSNDAEEDEQEKAGKPEAKVTSHTKSVYDNGETLDISLPIHPKSHIPQGKQDRWVVKLPDFLDINAEPFDPRPFEMNVKTHEDKNQELLDKLIAVNTVRWRYAKSETGGIFKETNSQIIQWEDGTYSLRVGSEIFDMFTTNTDDNYLVSEHNEEGILMTESTLSKSVKLVPASFQSTTHQKLAKALSAKQKKESYARSVVTKEDPEERQRRLESQENERYRLERRRKQAEEEEDYDSYAVSTSRSRPSRASQMYNAADEDDDDDDVAIGRTLASRRNNGYEDDGFIIDDEEEEEAVENDSADEESENEGDDDEEDDEEAAERLNRLKRAGASKYTNEGEQAQSEPVKSEEADNASQRDDAPRKKRRVILDDDEEEEE
Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p X 395 Homo Sapiens , Komagataella Phaffii , Synthetic Construct MKDHLIHNHHKHEHAHAEHLYFQGSSGSSGMSEPLIALRQAIKDKKPVGVNEGETIGNAKVLNIGEKQYSLDAPTSFVINGKEFNLKVIYQCWVFRDSSSADYITECEKENIDGISFVERSELISWLKGEITSSAFIKGEKVGITEENGKNEGETKSNNKRKLSDDPLLKEIASNERVLIDHNKVLRGLKPKDFSSVAKDCELRILKEKPANAKSSDSNGRSSTSVSSSSKDARNKEPIIVLSPAASSLVRMSNVKEFLQEGKFLDPSKEPASSSNLLAIQRKSSRFKTPIKLLVVDNVEKLFTKSEYWDRVVAIVTTGKDWQFKNYKYKDPQILFQKFNGFYFKYKGDAVPASVKSWNVKVLDIDRVERFSDRQVVEQFWDTVENTLVAKRYKS
DNA-directed RNA polymerases I, II, and III subunit RPABC1 E 214 Homo Sapiens , Komagataella Phaffii , Synthetic Construct MEDNNRIISRLWRSFRTVKEMAADRGYFISQEEMDQSLEEFRSKICDSMGNPQRKLMSFLANPTPEALEKYSDLGTLWVEFCDEPSVGIKTMRNFCLRIQEKNFSTGIFIYQNNITPSANKMIPTVSPAIIETFQESDLVVNITHHELVPKHIRLSDGEKSQLLQRYKLKESQLPRIQREDPVARYLGLKRGQVVKIIRRSETSGRYASYRICL
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III F 155 Homo Sapiens , Komagataella Phaffii , Synthetic Construct MSEDEAFNEQTENFENFEDEHFSDDNFEDRSTQPEDYAVGVTADGRQIINGDGIQEVNGTIKAHRKRSNKELAILKEERTTTPYLTKYERARILGTRALQISMNAPVLVDIEGETDPLQIAMKELSQRKIPLVIRRYLPDGSYEDWGCDELIVDN
RNA polymerase II third largest subunit B44, part of central core C 304 Homo Sapiens , Komagataella Phaffii , Synthetic Construct MSKEPKVNIINAQDDEVELMLSDVNLSLANSLRRTMLAEVPTLAIDLVEIKMNTSVLADEFISHRLGLIPLVSEDVEEMKYSRDCTCEDYCDECSVVLELSARHEGEEGTTDVYSSSLIKVSGPGNLNVGEPVRRDDYDQGILLCKLRNHQELNIRCIAKKGIAKEHAKWSPCSAIAFEYDPHNKLKHTDFWFEVDAKKEWPDSKYATWEEPPKPGEVFDYKAKPNRFYMTVETTGSLKANQVFSRGIKTLQEKLANVLFELENSRPANTTAYGGATAYGGQTVYGRETSYGGNTNYGDYNAPY
RNA polymerase II subunit G 171 Homo Sapiens , Komagataella Phaffii , Synthetic Construct MFFLKDLSLILTLHPSYFGPQMNQYLREKLLTDVEGTCTGQFGYIVTVLDGMNIDVGKGRIIPGSGSAEFEVKYRAVVWKPFKGEVVDAIVSNVSPIGFFADVGPLNVFVSTRLIPDNLVYNPSNSPPAYMSNDELITKGSKVRLKVVGTRTDVNEIYAIGSIKEDFLGAI
RNA polymerase II subunit B32 D 186 Homo Sapiens , Komagataella Phaffii , Synthetic Construct MNVSTSTVGARRRRAKQQVDDEENATLLRLGPEFALKQYDHDGNEHDLIALSLSESRLLIREALKARSRARNGGVDIESSNGEIDDDELAKVTSGAVANGVVKKTLDYLNTFARFKDEETCTAVDQLLHNSSDCSVLHPFEIAQLSSLGCEDVDEAITLIPSLAAKKEVNLQRILDELNRLEDPYK
DNA-directed RNA polymerases I, II, and III subunit RPABC3 H 145 Homo Sapiens , Komagataella Phaffii , Synthetic Construct MSSALFDDIFTVQTVDNGRYNKVSRIIGISTTNSAIKLTLDINNEMFPVSQDDSLTVTLANSLSLDGEDESANFSKSWRPPKPTDKSLADDYDYVMFGTVYKFEEGDEDKIKVYVSFGGLLMCLEGGYKSLASLKQDNLYILIRR
DNA-directed RNA polymerase subunit I 115 Homo Sapiens , Komagataella Phaffii , Synthetic Construct MASFRFCLECNNMLYPKEDKENQRLLYSCRNCDYTELAEDPKVYRHELITNIGETAGIVDDIGQDPTLPRSDKECPECHSRDCVFFQSQQRRKDTNMTLFYVCLNCKKTFRDESE

Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
RNA (5'-R(P*GP*CP*UP*UP*GP*UP*GP*CP*UP*GP*UP*CP*UP*UP*CP*GP*UP*CP*CP*A)-3') p 20 NA GCUUGUGCUGUCUUCGUCCA
DNA (198-MER) t 198 NA ATCAGAATCCCGGTGCCGAGGCCGCTCTTTTGGACGAAGACAGCACAAGCACCGCAAAAACGCACGAACGCGCAGACCCCCGCGAAAAAACCGCCAAGGGGAAAACACCCAAGACACCAGGCACGAGACAGAAAAAAACAACGAAAACGGCCACCACCCAAACACACCAAACACAAGAGCTAATTGACTGACGTAAGC
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2022-05-15
Deposition Author(s): Ehara, H. , Kujirai, T. , Kurumizaka, H. , Sekine, S. , Shirouzu, M.