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FASTA Sequence PDB Format mmCIF Format
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5FMF

The p-lobe of rna polymerase ii pre-initiation complex

PDB DOI: 10.2210/pdb5fmf/pdb

Classification: TRANSCRIPTION
Organism(s): Saccharomyces Cerevisiae

Deposited: 2015-11-03
Deposition Author(s): Asturias, F.J. , Bushnell, D.A. , Kalisman, N. , Kornberg, R.D. , Murakami, K. , Tsai, K.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.0 Å

5fmf
Literature

The p-lobe of rna polymerase ii pre-initiation complex

Asturias, F.J. , Bushnell, D.A. , Kalisman, N. , Kornberg, R.D. , Murakami, K. , Tsai, K.

Primary Citation of Related Structures: 5FMF


Proteins
Molecule Chains Sequence Length Organism Sequence
DNA REPAIR HELICASE RAD25, SSL2 1 492 Saccharomyces Cerevisiae SAVIGGDNEREEEDDDIDAVHSFEIANESVEVVKKRCQEIDYPVLEEYDFRNDHRNPDLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTIKKSVIVLCTSSVSVMQWRQQFLQWCTLQPENCAVFTSDNKEMFQTESGLVVSTYSMVANTRNRSHDSQKVMDFLTGREWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVREDDKIGDLNFLIGPKLYEANWMELSQKGHIANVQCAEVWCPMTAEFYQEYLRETARKRMLLYIMNPTKFQACQFLIQYHERRGDKIIVFSDNVYALQEYALKMGKPFIYGSTPQQERMNILQNFQYNDQINTIFLSKVGDTSIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRRNDEGFNAFFYSLVSKDTQEMYYSTKRQAFLVDQGYAFKVITHLHGMENIPNLAYASPRERRELLQEVLLKNEEAAGIEVGDDADNSVGR
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3, RPB8 H 146 Saccharomyces Cerevisiae MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 I 119 Saccharomyces Cerevisiae TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5, RPB10 J 65 Saccharomyces Cerevisiae MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNP
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 K 115 Saccharomyces Cerevisiae MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLA
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4, RPB12 L 46 Saccharomyces Cerevisiae ATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR
RNA POLYMERASE II PRE-INITIATION COMPLEX, TOA1 M 116 Saccharomyces Cerevisiae SNAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKVTTFSWDNQFNDYLISEDGPDENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEWV
TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 2, TOA2 O 122 Saccharomyces Cerevisiae MAVPGYYELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLTVKGNLDTYGFCDDVWTFIVKNCQVTVEDSHRDASQNGSGDSQSVISVDKLRIVACNSKKSE
TRANSCRIPTION INITIATION FACTOR IIB, SUA7 P 345 Saccharomyces Cerevisiae MMTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEASNPLLDGNNLSTRIGKGETTDMRFTKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLIHVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVTEGTIKSGYKILYEHRDKLVDPQLIANGVVSLDNLPGVEKK
TATA-BOX-BINDING PROTEIN, TBP Q 180 Saccharomyces Cerevisiae SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM
TRANSCRIPTION ELONGATION FACTOR S-II, DST1 2 174 Saccharomyces Cerevisiae NDGVDTAIYHHKLRDQVLKALYDVLAKESEHPPQSILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWKFS
TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ALPHA, TFA1 R 160 Saccharomyces Cerevisiae MDRPIDDIVKNLLKFVVRGFYGGSFVLVLDAILFHSVLAEDDLKQLLSINKTELGPLIARLRSDRLISIHKQREYPPNSKSVERVYYYVKYPHAIDAIKWKVHQVVQRLKDDLDKNSEPNGYMCPICLTKYTQLEAVQLLNFDRTEFLCSLCDEPLVEDD
TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT BETA, TFA2 S 123 Saccharomyces Cerevisiae SSKLLWATEYIQKKGKPVLVNELLDYLSMKKDDKVIELLKKLDRIEFDPKKGTFKYLSTYDVHSPSELLKLLRSQVTFKGISCKDLKDGWPQCDETINQLEEDSKILVLRTKKDKTPRYVWYN
RNA POLYMERASE II PRE-INITIATION COMPLEX, TFG1 U 150 Saccharomyces Cerevisiae DPNEYNEFPLRAPKEDLERTHLLKFQSKKKINPVTHLPVRLHRKDTRNLQFQLADVAGNLRRKTRQLKVLENAKKLRFEFYPWVMEDFDGYNTWVGSYEAGNSDSYVLLSVEDDGSFTMIPADKVYKFTARNKYATLTIDEAEKRMDKKS
TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT BETA, TFG2 V 174 Saccharomyces Cerevisiae EESLDLDLERSNRQVWLVRLPMFLAEKWRDRNNLHGQELGKIRINKDGSKITLLLNENDNDSIPHEYDLELTKKVVENEYVFTEQNLKKTAIVGTVCHECQVMPSSIRMPKKEILDYLFKLFDEYDYWSLKGLKERTRQPEAHLKECLDKVATLVKKGPYAFKYTLRPEYKKLK
RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 2, TFB2 W 62 Saccharomyces Cerevisiae ELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNSQVLDFAKRK
RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 5, TFB5 X 63 Saccharomyces Cerevisiae ARARKGALVQCDPSIKALILQIDAKMSDIVLEELDDTHLLVNPSKVEFVKHELNRLLSKNIYN
DNA REPAIR HELICASE RAD3 Y 778 Saccharomyces Cerevisiae MKFYIDDLPVLFPYPKIYPEQYNYMCDIKKTLDVGGNSILEMPSGTGKTVSLLSLTIAYQMHYPEHRKIIYCSRTMSEIEKALVELENLMDYRTKELGYQEDFRGLGLTSRKNLCLHPEVSKERKGTVVDEKCRRMTNGQAKRKLEEDPEANVELCEYHENLYNIEVEDYLPKGVFSFEKLLKYCEEKTLCPYFIVRRMISLCNIIIYSYHYLLDPKIAERVSNEVSKDSIVIFDEAHNIDNVCIESLSLDLTTDALRRATRGANALDERISEVRKVDSQKLQDEYEKLVQGLHSADILTDQEEPFVETPVLPQDLLTEAIPGNIRRAEHFVSFLKRLIEYLKTRMKVLHVISETPKSFLQHLKQLTFIERKPLRFCSERLSLLVRTLEVTEVEDFTALKDIATFATLISTYEEGFLLIIEPYEIENAAVPNPIMRFTCLDASIAIKPVFERFSSVIITSGTISPLDMYPRMLNFKTVLQKSYAMTLAKKSFLPMIITKGSDQVAISSRFEIRNDPSIVRNYGSMLVEFAKITPDGMVVFFPSYLYMESIVSMWQTMGILDEVWKHKLILVETPDAQETSLALETYRKACSNGRGAILLSVARGKVSEGIDFDHQYGRTVLMIGIPFQYTESRILKARLEFMRENYRIRENDFLSFDAMRHAAQCLGRVLRGKDDYGVMVLADRRFSRKRSQLPKWIAQGLSDADLNLSTDMAISNTKQFLRTMAQPTDPKDQEGVSVWSYEDLIKHQNSRKDQGGFIENENKEGEQDEDEDEDIEMQ
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 A 1733 Saccharomyces Cerevisiae MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 B 1224 Saccharomyces Cerevisiae MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 C 266 Saccharomyces Cerevisiae EEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQD
RNA POLYMERASE II PRE-INITIATION COMPLEX, RPB4 D 178 Saccharomyces Cerevisiae VSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKTREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1, RPB5 E 214 Saccharomyces Cerevisiae DQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2, RPB6 F 84 Saccharomyces Cerevisiae KAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 G 171 Saccharomyces Cerevisiae MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI

Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
NON-TEMPLATE STRAND DNA n 72 NA AAAAAAAAAAGGCGCCTATAAAAGGGGTTTCAATGTATCTATAACCAGGCATAAGTACTAAAGGGGGTGGGG
TEMPLATE STRAND DNA t 72 NA CCCCACCCCCTTTAGTACTTATGCCTGGTTATAGATACATTGAAACCCCTTTTATAGGCGCCTTTTTTTTTT
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2015-11-03
Deposition Author(s): Asturias, F.J. , Bushnell, D.A. , Kalisman, N. , Kornberg, R.D. , Murakami, K. , Tsai, K.