2024-05-15 REL PDBe PDBe PDBe 2018-07-26 2018-08-29 2018-08-29 2024-05-15 Spanish Ministry of Economy and Competitiveness BFU2013-48374-P Spain Spanish Ministry of Economy and Competitiveness BFU2017-87397-P Spain Yeast RNA polymerase I elongation complex stalled by cyclobutane pyrimidine dimer (CPD) Sanz-Murillo M Xu J RNA Polymerase I, UV-damage, stalling, Cyclobutane Pyrimidine Dimers (CPD), TRANSCRIPTION Sanz-Murillo M Xu J Belogurov GA Calvo O Gil-Carton D Moreno-Morcillo M Wang D Fernandez-Tornero C Structural basis of RNA polymerase I stalling at UV light-induced DNA damage. Proc. Natl. Acad. Sci. U.S.A. US 115 8972 8977 2018 30127008 doi:10.1073/pnas.1802626115 1091-6490 0040 PNASA6 6h67 FULLOVERLAP RNA Polymerase I stalling at DNA damage RNA Polymerase I stalling at DNA damage 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 0.631 RNA Polymerase I stalling at DNA damage 1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Saccharomyces cerevisiae S288C RNA Polymerase I stalling at DNA damage 1 15 16 17 Saccharomyces cerevisiae 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 DNA-directed RNA polymerase I subunit RPA49 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.046721707 1 LEVO MSVKRSVSEIEIESVQDQPSVAVGSFFKGFRAPSDTTFDLYKKKKSEKDEFVLHGENERLEYEGYTDSSSQASNQYVVGL FNPEKKSIQLYKAPVLVSKVVSKSSKNLRGPKIKSKSDTRPSALRNALGEAFGTKKAKKAIADLERNRIDSDKLTDSAID IVDSVRTASKDLPTRAQLDEITSNDRPTPLANIDATDVEQIYPIESIIPKKELQFIRVSSILKEADKEKKLELFPYQNNS KYVAKKLDSLTQPSQMTKLQLLYYLSLLLGVYENRRVNNKTKLLERLNSPPEILVDGILSRFTVIKPGQFGRSKDRSYFI DPQNEDKILCYILAIIMHLDNFIVEITPLAHELNLKPSKVVSLFRVLGAIVKGATVAQAEAFGIPKSTAASYKIATMKVP FKLPEMTRRGRGPRR Q01080 DNA-directed RNA polymerase I subunit RPA34 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.026933518 1 LEVO MSKLSKDYVSDSDSDDEVISNEFSIPDGFKKCKHLKNFPLNGDNKKKAKQQQVWLIKFPSNVDISKLKSLPVDFESSTTM TIDKHDYKIMDDTDIESSLTQDNLSNMTLLVPSESKESLKIASTAKDNAPLQFDKVFSVSETAKIPAIDYSKVRVPRKDV PKVEGLKLEHFATGYDAEDFHVAEEVKENKKEPKKRSHHDDEEESSEKKKKKKEKREKREKKDKKDKKKKHRD P47006 RNA Saccharomyces cerevisiae 0.003264036 1 AUCGAGAGGA Template DNA Saccharomyces cerevisiae 0.015816095999999998
Cyclobutane Pyrimidine Dimer at position 18 of the DNA sequence.
1 (DC)(DG)(DC)(DT)(DC)(DT)(DG)(DC)(DT)(DC)(DC)(DT)(DT)(DC)(DT)(DC)(DC)(TTD)(DT) (DC)(DC)(DT)(DC)(DT)(DC)(DG)(DA)(DT)(DG)(DG)(DC)(DT)(DA)(DT)(DG)(DA)(DG)(DA)(DT) (DC)(DA)(DA)(DC)(DT)(DA)(DG)(DG)(DC)(DT)(DG)(DC) DNA Non-template DNA Saccharomyces cerevisiae 0.016039287 1 (DG)(DC)(DA)(DG)(DC)(DC)(DT)(DA)(DG)(DT)(DT)(DG)(DA)(DT)(DC)(DT)(DC)(DA)(DT)(DA) (DG)(DC)(DC)(DC)(DA)(DT)(DT)(DC)(DC)(DT)(DA)(DC)(DT)(DC)(DA)(DG)(DG)(DA)(DG)(DA) (DA)(DG)(DG)(DA)(DG)(DC)(DA)(DG)(DA)(DG)(DC)(DG) DNA ZINC ION 6.5409e-05 6 ZN MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 0.22 8.0 10.0 C8H18N2O4S 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid 150.0 NaCl Sodium Chloride 5.0 C4H10O2S2 (2S,3S)-1,4-Bis(sulfanyl)butane-2,3-diol Quantifoil R2/1 COPPER 400 GLOW DISCHARGE ETHANE 95 277.15 FEI VITROBOT MARK III FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.5 4.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 1 2056 5.25 1 1500 4C3I C1 3.6 FSC 0.143 CUT-OFF RELION 2.0.5 254079 ANGULAR RECONSTITUTION RELION 2.0.5 ANGULAR RECONSTITUTION RELION 2.0.5 RELION 2.0.5 emd_0146.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 305.27997 305.27997 305.27997 90.0 90.0 90.0 X Y Z -0.053961135 0.09728247 -0.0000076939095 0.0040034503 1.06 1.06 1.06 0.0162 AUTHOR 4C3I PDB experimental model 5M3F PDB experimental model AB INITIO MODEL REAL 93.900000000000006