Yeast RNA polymerase I* elongation complex bound to nucleotide analog GMPCPP

2024-05-15 REL PDBe PDBe PDBe 2018-09-11 2018-10-24 2019-04-03 2024-05-15 European Research Council ERC-2013-AdG340964-POL1PIC Germany Yeast RNA polymerase I* elongation complex bound to nucleotide analog GMPCPP Tafur L Sadian Y transcription, polymerase, nucleotide, elongation Tafur L Sadian Y Hanske J Wetzel R Weis F Muller CW The cryo-EM structure of a 12-subunit variant of RNA polymerase I reveals dissociation of the A49-A34.5 heterodimer and rearrangement of subunit A12.2. Elife US 8 2019 30913026 doi:10.7554/eLife.43204 2050-084X EMD-0238 other EM volume 6hlq FULLOVERLAP Yeast RNA polymerase I* elongation complex bound to nucleotide analog GMPCPP Yeast RNA polymerase I* elongation complex bound to nucleotide analog GMPCPP 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Yeast RNA polymerase I* 1 1 2 3 4 5 6 7 8 9 10 11 12 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) nucleic acids 1 13 14 15 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) DNA-directed RNA polymerase I subunit RPA190 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.186676969 1 LEVO MDISKPVGSEITSVDFGILTAKEIRNLSAKQITNPTVLDNLGHPVSGGLYDLALGAFLRNLCSTCGLDEKFCPGHQGHIE LPVPCYNPLFFNQLYIYLRASCLFCHHFRLKSVEVHRYACKLRLLQYGLIDESYKLDEITLGSLNSSMYTDDEAIEDNED EMDGEGSKQSKDISSTLLNELKSKRSEYVDMAIAKALSDGRTTERGSFTATVNDERKKLVHEFHKKLLSRGKCDNCGMFS PKFRKDGFTKIFETALNEKQITNNRVKGFIRQDMIKKQKQAKKLDGSNEASANDEESFDVGRNPTTRPKTGSTYILSTEV KNILDTVFRKEQCVLQYVFHSRPNLSRKLVKADSFFMDVLVVPPTRFRLPSKLGEEVHENSQNQLLSKVLTTSLLIRDLN DDLSKLQKDKVSLEDRRVIFSRLMNAFVTIQNDVNAFIDSTKAQGRTSGKVPIPGVKQALEKKEGLFRKHMMGKRVNYAA RSVISPDPNIETNEIGVPPVFAVKLTYPEPVTAYNIAELRQAVINGPDKWPGATQIQNEDGSLVSLIGMSVEQRKALANQ LLTPSSNVSTHTLNKKVYRHIKNRDVVLMNRQPTLHKASMMGHKVRVLPNEKTLRLHYANTGAYNADFDGDEMNMHFPQN ENARAEALNLANTDSQYLTPTSGSPVRGLIQDHISAGVWLTSKDSFFTREQYQQYIYGCIRPEDGHTTRSKIVTLPPTIF KPYPLWTGKQIITTVLLNVTPPDMPGINLISKNKIKNEYWGKGSLENEVLFKDGALLCGILDKSQYGASKYGIVHSLHEV YGPEVAAKVLSVLGRLFTNYITATAFTCGMDDLRLTAEGNKWRTDILKTSVDTGREAAAEVTNLDKDTPADDPELLKRLQ EILRDNNKSGILDAVTSSKVNAITSQVVSKCVPDGTMKKFPCNSMQAMALSGAKGSNVNVSQIMCLLGQQALEGRRVPVM VSGKTLPSFKPYETDAMAGGYVKGRFYSGIKPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLTKQLEGVHVSYDNSIRD ADGTLVQFMYGGDAIDITKESHMTQFEFCLDNYYALLKKYNPSALIEHLDVESALKYSKKTLKYRKKHSKEPHYKQSVKY DPVLAKYNPAKYLGSVSENFQDKLESFLDKNSKLFKSSDGVNEKKFRALMQLKYMRSLINPGEAVGIIASQSVGEPSTQM TLNTFHFAGHGAANVTLGIPRLREIVMTASAAIKTPQMTLPIWNDVSDEQADTFCKSISKVLLSEVIDKVIVTETTGTSN TAGGNAARSYVIHMRFFDNNEYSEEYDVSKEELQNVISNQFIHLLEAAIVKEIKKQKRTTGPDIGVAVPRLQTDVANSSS NSKRLEEDNDEEQSHKKTKQAVSYDEPDEDEIETMREAEKSSDEEGIDSDKESDSDSEDEDVDMNEQINKSIVEANNNMN KVQRDRQSAIISHHRFITKYNFDDESGKWCEFKLELAADTEKLLMVNIVEEICRKSIIRQIPHIDRCVHPEPENGKRVLV TEGVNFQAMWDQEAFIDVDGITSNDVAAVLKTYGVEAARNTIVNEINNVFSRYAISVSFRHLDLIADMMTRQGTYLAFNR QGMETSTSSFMKMSYETTCQFLTKAVLDNEREQLDSPSARIVVGKLNNVGTGSFDVLAKVPNAA P10964 2.7.7.6 DNA-directed RNA polymerase I subunit RPA135 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.135910328 1 LEVO MSKVIKPPGQARTADFRTLERESRFINPPKDKSAFPLLQEAVQPHIGSFNALTEGPDGGLLNLGVKDIGEKVIFDGKPLN SEDEISNSGYLGNKLSVSVEQVSIAKPMSNDGVSSAVERKVYPSESRQRLTSYRGKLLLKLKWSVNNGEENLFEVRDCGG LPVMLQSNRCHLNKMSPYELVQHKEESDEIGGYFIVNGIEKLIRMLIVQRRNHPMAIIRPSFANRGASYSHYGIQIRSVR PDQTSQTNVLHYLNDGQVTFRFSWRKNEYLVPVVMILKALCHTSDREIFDGIIGNDVKDSFLTDRLELLLRGFKKRYPHL QNRTQVLQYLGDKFRVVFQASPDQSDLEVGQEVLDRIVLVHLGKDGSQDKFRMLLFMIRKLYSLVAGECSPDNPDATQHQ EVLLGGFLYGMILKEKIDEYLQNIIAQVRMDINRGMAINFKDKRYMSRVLMRVNENIGSKMQYFLSTGNLVSQSGLDLQQ VSGYTVVAEKINFYRFISHFRMVHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCGLLNHFAHKCRISTQQSDVSR IPSILYSLGVAPASHTFAAGPSLCCVQIDGKIIGWVSHEQGKIIADTLRYWKVEGKTPGLPIDLEIGYVPPSTRGQYPGL YLFGGHSRMLRPVRYLPLDKEDIVGPFEQVYMNIAVTPQEIQNNVHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQ MGKQTMGTPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYTGYDMDDAMIINKSADERGFGY GTMYKTEKVDLALNRNRGDPITQHFGFGNDEWPKEWLEKLDEDGLPYIGTYVEEGDPICAYFDDTLNKTKIKTYHSSEPA YIEEVNLIGDESNKFQELQTVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTI GMFVESLAGKAGALHGIAQDSTPWIFNEDDTPADYFGEQLAKAGYNYHGNEPMYSGATGEELRADIYVGVVYYQRLRHMV NDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRLLNSSDYTQASVCRECGSILTTQQSVPRI GSISTVCCRRCSMRFEDAKKLLTKSEDGEKIFIDDSQIWEDGQGNKFVGGNETTTVAIPFVLKYLDSELSAMGIRLRYNV EPK P22138 2.7.7.6 DNA-directed RNA polymerases I and III subunit RPAC1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.037732613 1 LEVO MSNIVGIEYNRVTNTTSTDFPGFSKDAENEWNVEKFKKDFEVNISSLDAREANFDLINIDTSIANAFRRIMISEVPSVAA EYVYFFNNTSVIQDEVLAHRIGLVPLKVDPDMLTWVDSNLPDDEKFTDENTIVLSLNVKCTRNPDAPKGSTDPKELYNNA HVYARDLKFEPQGRQSTTFADCPVVPADPDILLAKLRPGQEISLKAHCILGIGGDHAKFSPVSTASYRLLPQINILQPIK GESARRFQKCFPPGVIGIDEGSDEAYVKDARKDTVSREVLRYEEFADKVKLGRVRNHFIFNVESAGAMTPEEIFFKSVRI LKNKAEYLKNCPITQ P07703 DNA-directed RNA polymerase I subunit RPA14 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.014599128 1 LEVO MMKGSRRTGNNTATTLNTPVVIHATQLPQHVSTDEVLQFLESFIDEKENIIDSTTMNTISGNAADADAAAVANTSLNIDT NLSSSISQLKRIQRDFKGLPPAQDFSAAPIQVSTTEKKETSIGVSATGGKKTTFADE P50106 DNA-directed RNA polymerases I, II, and III subunit RPABC1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.025117094 1 LEVO MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWV EFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDE KRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM P20434 DNA-directed RNA polymerases I, II, and III subunit RPABC2 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.017931833999999997 1 LEVO MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRA TTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL P20435 DNA-directed RNA polymerase I subunit RPA43 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.036264852 1 LEVO MSQVKRANENRETARFIKKHKKQVTNPIDEKNGTSNCIVRVPIALYVSLAPMYLENPLQGVMKQHLNPLVMKYNNKVGGV VLGYEGLKILDADPLSKEDTSEKLIKITPDTPFGFTWCHVNLYVWQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKN NIPVDWTFVHNDVEEDADVINTDENNGNNNNEDNKDSNGGSNSLGKFSFGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTG RVVSVDGTLISDADEEGNGYNSSRSQAESLPIVSNKKIVFDDEVSIENKESHKELDLPEVKEDNGSEIVYEENTSESNDG ESSDSD P46669 DNA-directed RNA polymerases I, II, and III subunit RPABC3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.016525363 1 LEVO MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWR PPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR P20436 DNA-directed RNA polymerase I subunit RPA12 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.013676566 1 LEVO MSVVGSLIFCLDCGDLLENPNAVLGSNVECSQCKAIYPKSQFSNLKVVTTTADDAFPSSLRAKKSVVKTSLKKNELKDGA TIKEKCPQCGNEEMNYHTLQLRSADEGATVFYTCTSCGYKFRTNN P32529 DNA-directed RNA polymerases I, II, and III subunit RPABC5 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.008290732 1 LEVO MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD P22139 DNA-directed RNA polymerases I and III subunit RPAC2 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.01616786 1 LEVO MTEDIEQKKTATEVTPQEPKHIQEEEEQDVDMTGDEEQEEEPDREKIKLLTQATSEDGTSASFQIVEEDHTLGNALRYVI MKNPDVEFCGYSIPHPSENLLNIRIQTYGETTAVDALQKGLKDLMDLCDVVESKFTEKIKSM P28000 DNA-directed RNA polymerases I, II, and III subunit RPABC4 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.007729969 1 LEVO MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR P40422 RNA Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.006414902 1 UAUAUGCAUAAAGACCAGGC Non-template strand Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.011756599999999999 1 (DG)(DG)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DA)(DG)(DT)(DA)(DA)(DA)(DC)(DT)(DA)(DG)(DT) (DA)(DT)(DT)(DG)(DA)(DA)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DG)(DA)(DC)(DT)(DT) DNA Template strand Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.011629489 1 (DA)(DA)(DG)(DT)(DC)(DA)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DA)(DC)(DG)(DC)(DC)(DT)(DG) (DG)(DT)(DC)(DA)(DT)(DT)(DA)(DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT)(DG)(DC)(DC) DNA ZINC ION 6.5409e-05 7 ZN MAGNESIUM ION 2.4305e-05 1 MG PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER 0.0005212079999999999 1 G2P singleParticle particle 0.1 7.5 ETHANE 100 277 FEI VITROBOT MARK IV

30 seconds incubation 3 seconds blotting blotting force 3.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) 39.0 1 5M5X C1 3.18 FSC 0.143 CUT-OFF RELION 2 182488 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_0239.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 260 260 260 0 0 0 260 260 260 270.4 270.4 270.4 90.0 90.0 90.0 X Y Z -0.30583996 0.44941378 -0.0002841761 0.020126564 1.04 1.04 1.04 0.066 AUTHOR ::::EMDATABANK.org::::EMD-0239:::: Yeast RNA polymerase I* elongation complex bound to nucleotide analog GMPCPP 5M5X PDB experimental model 4C3I PDB experimental model 4C2M PDB experimental model 4A3J PDB experimental model 2E2J PDB experimental model RIGID BODY FIT

Initial rigid body fitting was done in Chimera and model building was done in Coot.

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