Monomeric RNA polymerase I at 4.9 A resolution

2024-05-15 REL PDBe PDBe PDBe 2016-10-11 2016-10-19 2017-03-22 2024-05-15 Spanish Ministry of Economy and Competitiveness BFU2013-48374-P Spain Ramon Areces Foundation Spain Monomeric RNA polymerase I at 4.9 A resolution Torreira E Louro JA Gil-Carton D Gallego O Calvo O Fernandez-Tornero C Multi-protein complex, RNA polymerase, Monomeric form, Transcription Torreira E Louro JA Pazos I Gonzalez-Polo N Gil-Carton D Duran AG Tosi S Gallego O Calvo O Fernandez-Tornero C The dynamic assembly of distinct RNA polymerase I complexes modulates rDNA transcription. Elife US 6 2017 28262097 doi:10.7554/eLife.20832 2050-084X 5lmx unknown S. cerevisiae RNA polymerase I in the monomeric state S. cerevisiae RNA polymerase I in the monomeric state 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Saccharomyces cerevisiae 0.594 DNA-directed RNA polymerase I subunit RPA190 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 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) 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,DNA-directed RNA polymerases I and III subunit RPAC1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.042850402 1 LEVO MSNIVGIEYNRVTNTTSTDFPGFSKDAENEWNVEKFKKDFEVNISSLDAREANFDLINIDTSIANAFRRIMISEVPSVAA EYVYFFNNTSVIQDEVLAHRIGLVPLKVDPDMLTWVDSNLPDDEKFTDENTIVLSLNVKCTRNPDAPKGSTDPKELYNNA HVYARDLKFEPQGRQSTTFADCPVVPADPDILLAKLRPGQEISLKAHCILGIGGDHAKFSPVSTASYRLLPQINILQPIK GESARRFQKCFPPGVIGIDEGSDEAYVKDARKDTVSREVLRYEEFADKVKLGRVRNHFIFNVESAGAMTPEEIFFKSVRI LKNKAEYLKNCPITQGSMEKRRWKKNFIAVSAANRFKKISSSGALDYDIPTTASENLYFQ P07703 DNA-directed RNA polymerase I subunit RPA14 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 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) 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) ATCC 204508 / S288c 0.017931833999999997 1 LEVO MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRA TTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL P20435 DNA-directed RNA polymerase I subunit RPA43 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 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) ATCC 204508 / S288c 0.016525363 1 LEVO MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWR PPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR P20436 DNA-directed RNA polymerase I subunit RPA12 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 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) ATCC 204508 / S288c 0.008290732 1 LEVO MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD P22139 DNA-directed RNA polymerases I and III subunit RPAC2 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 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) ATCC 204508 / S288c 0.007729969 1 LEVO MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR P40422 DNA-directed RNA polymerase I subunit RPA49 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 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) ATCC 204508 / S288c 0.026933518 1 LEVO MSKLSKDYVSDSDSDDEVISNEFSIPDGFKKCKHLKNFPLNGDNKKKAKQQQVWLIKFPSNVDISKLKSLPVDFESSTTM TIDKHDYKIMDDTDIESSLTQDNLSNMTLLVPSESKESLKIASTAKDNAPLQFDKVFSVSETAKIPAIDYSKVRVPRKDV PKVEGLKLEHFATGYDAEDFHVAEEVKENKKEPKKRSHHDDEEESSEKKKKKKEKREKREKKDKKDKKKKHRD P47006 ZINC ION 6.5409e-05 6 ZN singleParticle particle 0.06 7.8 20.0 HEPES 100.0 NaCl Quantifoil R2/2 COPPER 400 CARBON HOLEY ARRAY GLOW DISCHARGE 60 ETHANE 95 277 FEI VITROBOT MARK III FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.0 1.9000000000000001 4.2 47000.0 79096.0 FEI TITAN KRIOS AUTOGRID HOLDER FEI FALCON II (4k x 4k) COUNTING 1-68 1 1288 4.0 68.0 1 190750

Negative-staining reconstruction of RNA polymerase I

2 4.9 FSC 0.143 CUT-OFF RELION 1.4 122348 PROJECTION MATCHING PROJECTION MATCHING RELION 1.4 6 30000.0 RELION 1.4 emd_4088.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 162 162 162 0 0 0 162 162 162 286.74 286.74 286.74 90.0 90.0 90.0 X Y Z -0.18001063 0.40812755 0.0045005027 0.024201661 1.77 1.77 1.77 0.14 EMDB ::::EMDATABANK.org::::EMD-4088:::: RIGID BODY FIT REAL 111.0