Pol I Initial Transcribing Complex with a truncated scaffold at 6.9 angstrom

2019-12-25 REL RCSB RCSB RCSB 2017-06-16 2017-07-05 2017-07-05 2019-12-25 Northwestern University Cornew Innovation Award United States National Institutes of Health/National Cancer Institute (NIH/NCI) NCI 5K22CA184235 United States American Cancer Society IRG-15-173-21 United States National Science Foundation (NSF, United States) MCB-1149521 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) NIGMS GM110387 United States Pol I Initial Transcribing Complex with a truncated scaffold at 6.9 angstrom Han Y He Y Han Y Yan C Nguyen THD Jackobel AJ Ivanov I Knutson BA He Y Structural mechanism of ATP-independent transcription initiation by RNA polymerase I. Elife US 6 2017 28623663 doi:10.7554/eLife.27414 2050-084X EMD-8777 associated EM volume

RNA polymerase I Initial Transcribing Complex

EMD-8771 other EM volume EMD-8772 other EM volume EMD-8776 other EM volume EMD-8775 other EM volume EMD-8774 other EM volume EMD-8773 other EM volume RNA Polymerase I Initial Transcribing Complex with a truncated scaffold RNA Polymerase I Initial Transcribing Complex with a truncated scaffold 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 Saccharomyces cerevisiae S288c 0.9 DNA-directed RNA polymerase I subunit RPA190 Saccharomyces cerevisiae S288c LEVO MDISKPVGSEITSVDFGILTAKEIRNLSAKQITNPTVLDNLGHPVSGGLYDLALGAFLRN LCSTCGLDEKFCPGHQGHIELPVPCYNPLFFNQLYIYLRASCLFCHHFRLKSVEVHRYAC KLRLLQYGLIDESYKLDEITLGSLNSSMYTDDEAIEDNEDEMDGEGSKQSKDISSTLLNE LKSKRSEYVDMAIAKALSDGRTTERGSFTATVNDERKKLVHEFHKKLLSRGKCDNCGMFS PKFRKDGFTKIFETALNEKQITNNRVKGFIRQDMIKKQKQAKKLDGSNEASANDEESFDV GRNPTTRPKTGSTYILSTEVKNILDTVFRKEQCVLQYVFHSRPNLSRKLVKADSFFMDVL VVPPTRFRLPSKLGEEVHENSQNQLLSKVLTTSLLIRDLNDDLSKLQKDKVSLEDRRVIF SRLMNAFVTIQNDVNAFIDSTKAQGRTSGKVPIPGVKQALEKKEGLFRKHMMGKRVNYAA RSVISPDPNIETNEIGVPPVFAVKLTYPEPVTAYNIAELRQAVINGPDKWPGATQIQNED GSLVSLIGMSVEQRKALANQLLTPSSNVSTHTLNKKVYRHIKNRDVVLMNRQPTLHKASM MGHKVRVLPNEKTLRLHYANTGAYNADFDGDEMNMHFPQNENARAEALNLANTDSQYLTP TSGSPVRGLIQDHISAGVWLTSKDSFFTREQYQQYIYGCIRPEDGHTTRSKIVTLPPTIF KPYPLWTGKQIITTVLLNVTPPDMPGINLISKNKIKNEYWGKGSLENEVLFKDGALLCGI LDKSQYGASKYGIVHSLHEVYGPEVAAKVLSVLGRLFTNYITATAFTCGMDDLRLTAEGN KWRTDILKTSVDTGREAAAEVTNLDKDTPADDPELLKRLQEILRDNNKSGILDAVTSSKV NAITSQVVSKCVPDGTMKKFPCNSMQAMALSGAKGSNVNVSQIMCLLGQQALEGRRVPVM VSGKTLPSFKPYETDAMAGGYVKGRFYSGIKPQEYYFHCMAGREGLIDTAVKTSRSGYLQ RCLTKQLEGVHVSYDNSIRDADGTLVQFMYGGDAIDITKESHMTQFEFCLDNYYALLKKY NPSALIEHLDVESALKYSKKTLKYRKKHSKEPHYKQSVKYDPVLAKYNPAKYLGSVSENF QDKLESFLDKNSKLFKSSDGVNEKKFRALMQLKYMRSLINPGEAVGIIASQSVGEPSTQM TLNTFHFAGHGAANVTLGIPRLREIVMTASAAIKTPQMTLPIWNDVSDEQADTFCKSISK VLLSEVIDKVIVTETTGTSNTAGGNAARSYVIHMRFFDNNEYSEEYDVSKEELQNVISNQ FIHLLEAAIVKEIKKQKRTTGPDIGVAVPRLQTDVANSSSNSKRLEEDNDEEQSHKKTKQ AVSYDEPDEDEIETMREAEKSSDEEGIDSDKESDSDSEDEDVDMNEQINKSIVEANNNMN KVQRDRQSAIISHHRFITKYNFDDESGKWCEFKLELAADTEKLLMVNIVEEICRKSIIRQ IPHIDRCVHPEPENGKRVLVTEGVNFQAMWDQEAFIDVDGITSNDVAAVLKTYGVEAARN TIVNEINNVFSRYAISVSFRHLDLIADMMTRQGTYLAFNRQGMETSTSSFMKMSYETTCQ FLTKAVLDNEREQLDSPSARIVVGKLNNVGTGSFDVLAKVPNAA DNA-directed RNA polymerase I subunit RPA135 Saccharomyces cerevisiae S288c LEVO MSKVIKPPGQARTADFRTLERESRFINPPKDKSAFPLLQEAVQPHIGSFNALTEGPDGGL LNLGVKDIGEKVIFDGKPLNSEDEISNSGYLGNKLSVSVEQVSIAKPMSNDGVSSAVERK VYPSESRQRLTSYRGKLLLKLKWSVNNGEENLFEVRDCGGLPVMLQSNRCHLNKMSPYEL VQHKEESDEIGGYFIVNGIEKLIRMLIVQRRNHPMAIIRPSFANRGASYSHYGIQIRSVR PDQTSQTNVLHYLNDGQVTFRFSWRKNEYLVPVVMILKALCHTSDREIFDGIIGNDVKDS FLTDRLELLLRGFKKRYPHLQNRTQVLQYLGDKFRVVFQASPDQSDLEVGQEVLDRIVLV HLGKDGSQDKFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMILKEKIDEY LQNIIAQVRMDINRGMAINFKDKRYMSRVLMRVNENIGSKMQYFLSTGNLVSQSGLDLQQ VSGYTVVAEKINFYRFISHFRMVHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCG LLNHFAHKCRISTQQSDVSRIPSILYSLGVAPASHTFAAGPSLCCVQIDGKIIGWVSHEQ GKIIADTLRYWKVEGKTPGLPIDLEIGYVPPSTRGQYPGLYLFGGHSRMLRPVRYLPLDK EDIVGPFEQVYMNIAVTPQEIQNNVHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQ MGKQTMGTPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYTG YDMDDAMIINKSADERGFGYGTMYKTEKVDLALNRNRGDPITQHFGFGNDEWPKEWLEKL DEDGLPYIGTYVEEGDPICAYFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESNKFQELQT VSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTI GMFVESLAGKAGALHGIAQDSTPWIFNEDDTPADYFGEQLAKAGYNYHGNEPMYSGATGE ELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALI GHGTSFLLQDRLLNSSDYTQASVCRECGSILTTQQSVPRIGSISTVCCRRCSMRFEDAKK LLTKSEDGEKIFIDDSQIWEDGQGNKFVGGNETTTVAIPFVLKYLDSELSAMGIRLRYNV EPK DNA-directed RNA polymerases I and III subunit RPAC1 Saccharomyces cerevisiae S288c LEVO MSNIVGIEYNRVTNTTSTDFPGFSKDAENEWNVEKFKKDFEVNISSLDAREANFDLINID TSIANAFRRIMISEVPSVAAEYVYFFNNTSVIQDEVLAHRIGLVPLKVDPDMLTWVDSNL PDDEKFTDENTIVLSLNVKCTRNPDAPKGSTDPKELYNNAHVYARDLKFEPQGRQSTTFA DCPVVPADPDILLAKLRPGQEISLKAHCILGIGGDHAKFSPVSTASYRLLPQINILQPIK GESARRFQKCFPPGVIGIDEGSDEAYVKDARKDTVSREVLRYEEFADKVKLGRVRNHFIF NVESAGAMTPEEIFFKSVRILKNKAEYLKNCPITQ DNA-directed RNA polymerase I subunit RPA14 Saccharomyces cerevisiae S288c LEVO MMKGSRRTGNNTATTLNTPVVIHATQLPQHVSTDEVLQFLESFIDEKENIIDSTTMNTIS GNAADADAAAVANTSLNIDTNLSSSISQLKRIQRDFKGLPPAQDFSAAPIQVSTTEKKET SIGVSATGGKKTTFADE DNA-directed RNA polymerases I, II, and III subunit RPABC1 Saccharomyces cerevisiae S288c LEVO MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM DNA-directed RNA polymerases I, II, and III subunit RPABC2 Saccharomyces cerevisiae S288c LEVO MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL DNA-directed RNA polymerase I subunit RPA43 Saccharomyces cerevisiae S288c LEVO MSQVKRANENRETARFIKKHKKQVTNPIDEKNGTSNCIVRVPIALYVSLAPMYLENPLQG VMKQHLNPLVMKYNNKVGGVVLGYEGLKILDADPLSKEDTSEKLIKITPDTPFGFTWCHV NLYVWQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDVEEDADVI NTDENNGNNNNEDNKDSNGGSNSLGKFSFGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTG RVVSVDGTLISDADEEGNGYNSSRSQAESLPIVSNKKIVFDDEVSIENKESHKELDLPEV KEDNGSEIVYEENTSESNDGESSDSD DNA-directed RNA polymerases I, II, and III subunit RPABC3 Saccharomyces cerevisiae S288c LEVO MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG LLMRLEGNYRNLNNLKQENAYLLIRR DNA-directed RNA polymerase I subunit RPA12 Saccharomyces cerevisiae S288c LEVO MSVVGSLIFCLDCGDLLENPNAVLGSNVECSQCKAIYPKSQFSNLKVVTTTADDAFPSSL RAKKSVVKTSLKKNELKDGATIKEKCPQCGNEEMNYHTLQLRSADEGATVFYTCTSCGYK FRTNN DNA-directed RNA polymerases I, II, and III subunit RPABC5 Saccharomyces cerevisiae S288c LEVO MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF LRYNPLEKRD DNA-directed RNA polymerases I and III subunit RPAC2 Saccharomyces cerevisiae S288c LEVO MTEDIEQKKTATEVTPQEPKHIQEEEEQDVDMTGDEEQEEEPDREKIKLLTQATSEDGTS ASFQIVEEDHTLGNALRYVIMKNPDVEFCGYSIPHPSENLLNIRIQTYGETTAVDALQKG LKDLMDLCDVVESKFTEKIKSM DNA-directed RNA polymerases I, II, and III subunit RPABC4 Saccharomyces cerevisiae S288c LEVO MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKAR TKRLVQFEAR DNA-directed RNA polymerase I subunit RPA49 Saccharomyces cerevisiae S288c LEVO MSVKRSVSEIEIESVQDQPSVAVGSFFKGFRAPSDTTFDLYKKKKSEKDEFVLHGENERL EYEGYTDSSSQASNQYVVGLFNPEKKSIQLYKAPVLVSKVVSKSSKNLRGPKIKSKSDTR PSALRNALGEAFGTKKAKKAIADLERNRIDSDKLTDSAIDIVDSVRTASKDLPTRAQLDE ITSNDRPTPLANIDATDVEQIYPIESIIPKKELQFIRVSSILKEADKEKKLELFPYQNNS KYVAKKLDSLTQPSQMTKLQLLYYLSLLLGVYENRRVNNKTKLLERLNSPPEILVDGILS RFTVIKPGQFGRSKDRSYFIDPQNEDKILCYILAIIMHLDNFIVEITPLAHELNLKPSKV VSLFRVLGAIVKGATVAQAEAFGIPKSTAASYKIATMKVPFKLPEMTRRGRGPRR DNA-directed RNA polymerase I subunit RPA34 Saccharomyces cerevisiae S288c LEVO MSKLSKDYVSDSDSDDEVISNEFSIPDGFKKCKHLKNFPLNGDNKKKAKQQQVWLIKFPS NVDISKLKSLPVDFESSTTMTIDKHDYKIMDDTDIESSLTQDNLSNMTLLVPSESKESLK IASTAKDNAPLQFDKVFSVSETAKIPAIDYSKVRVPRKDVPKVEGLKLEHFATGYDAEDF HVAEEVKENKKEPKKRSHHDDEEESSEKKKKKKEKREKREKKDKKDKKKKHRD RNA polymerase I-specific transcription initiation factor RRN6 Saccharomyces cerevisiae S288c Escherichia coli LEVO MSEGQIPSSDVLGSQLGVGVQGASLYCPQENYTTKKQEKPQWLRPVDDTLAEDALDLHIV VKSLLCDTAIRYISDDKVLQESDADDDLITSDIDEDTDNQGDTSIVVNPVIPVVPKDVHF FKKVDVGNDSMFGVNCDTPVSFQDYIPSDLLRNLDDTLQESTNSSRPMQDAFFWDPTVAN RLDSQYIQTASDLRNYRDGTEIIAYASGKTGSVLNIAVLTRQNTLHLNRHNNVTSIELHS PIKSIKIPGASESIGRRSNLVGIITENSFQIFRIESVHSRSCDVMVSSSEPLYFVEIDDL QVVDFAFNPWDLQQFAIIDIKGNWSIGRIPKNFNNNNKRKLQLIDNLHGTIFDPEELSSW KRIEWFSHFQKILVFDRSKMIEIDFMNNWQTEVVQAKAWSNIRDYKRIDDKNGILLTSRE IIIVGASESNDPVRRISWKHDLDPDDTTLRITVQKVKKPDHILLVAFVYSMRHKRIYMHV FSHRKANLFQSLGCSTVLEIPGGTPTGIETILTLDHIDDESRREEDADENFELVVDFLVK LRNSSEVYYYALSNTQNSEPNKQETPIIVDHPEWASLFNNADEREKESIGALVSQIKLKE RERISRVQNLIEHENSHDEDKYLQDLGYRLSIATNELLESWQKTKDESILSGSLSHSKLK NLLENSDSFASIPEFSSLLDQFFQYYQDQDVTFIGFEKLLHLFLHEDVPGLDIFYNKLLQ CWVLVSPQAELLTKEIVKDIIWSLARLEKPSLFEPIQNEISRSLSGPYQDIISSWDMDDI NEEDESNEFNFDSQFSAPFNGRPPFNLNSQSQIPTIKSSQSSGLARRKRILKTQSQKATP LSQSTQNLSVLPDSMTPAFTLMQPPSSQISFVNDSQPRNSQKAKKKKKRIRGFG RNA polymerase I-specific transcription initiation factor RRN7 Saccharomyces cerevisiae S288c Escherichia coli LEVO MSTFIRGPICGTDNCPSRLWRIIDGRRTCQYGHVMEGDVEFNDDEDDLNGLGAGVITRRL NLTTNATGSFQSSQLTNSQLLQQQQRQSHKKFKKLIGHEAKLLFLKSFQFILKRQIRWLI TEMRFPKEFEHVAKIIWLKILKTINDQPQEELKLQLHMTSTISILYLASTHLSLPVYTCD YIKWICTAKMPYFQASEILPKSWRIQLPNYYVSILEGSISPFNGQLYNKIALTCGMIHFK EFFNSEISCQGLLLKLVMQCALPPEFYFYTKQVIEFEETDIRNLTLWERTDERHTGRVSN HAELRVLSYFMLTINWMLSFDRDRQYPLKWILSLTESLTQRTTTSESIGRNIVKVVYPDK PTSSDYFQWSEEETLEFLKWMEKQFLPTQTKSLHNENGSMEMTIDQKIARRKLYKIFPLD REANHDGEFNDSTHQLTFIEDLQERYAKQTPFFESNKIRDSLNYQEANPPARKEAIGRLL THIASQLLVDFAISKEQLKDCISRIKNACLHRMN RNA polymerase I-specific transcription initiation factor RRN11 Saccharomyces cerevisiae S288c Escherichia coli LEVO MFEVPITLTNRKFAQRRKLKYQYINYISRRFDRISKKSTTTDSLPTPENSAAENNDEEEG QNSEAGTYRRSVLQQKKRRRERHWRSVVGEIYSTTESETDSQEEETEEGGEHDTGIDKED SDEERKFWKKYEKPEKSFEIWRTVSSQNKQPINKQKMTYHNFKKIEKIPLRKMEIPLLHC TKENKLYFQSISRGLEPLKTSTSEVRNYRTRHIVTLTDLLHLNVSRHNWSLAYKIFATLI RIPGVQIKSLWGIGVEILDNLSNSSSGLDFLQWMCQIYSSKSRFVQNINYRSIVPPFQTG SRTHTAKFAITYLWSSLINCQKSMEPSSNIIDKPFDTENDLLQELIDKISEWVLTPPFME DAEVWFIYASCHLLKADTLSRQFVNDNKNNDLIGLDRDIKINQVIKHIHYVRTFLKICLD KGGFAVPSRLIENQLKSFESRLYGEAQDIQERDVANVYDSIDNSSVENSFGDVYETNAEF LDTQLMDLSPEDNGLDEMHYSDEDSSE RNA Saccharomyces cerevisiae S288c AUGCGA template strand DNA Saccharomyces cerevisiae S288c TGTCTTCAACTGCTTTCGCATGAAGTACCTCCCAACTACTTTTCCTCACACTTG DNA upstream non-template strand DNA Saccharomyces cerevisiae S288c TGAGGAAAAGTAGTTGGG DNA downstream non-template strand DNA Saccharomyces cerevisiae S288c GCAGTTGAAGACA DNA singleParticle particle 7.6 Quantifoil S7/2 COPPER 400 CARBON CONTINUOUS GLOW DISCHARGE AIR ETHANE 100 277

JEOL 3200FS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.0 2.0 5.0 15000.0 GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 12.0 17.2 1 Gctf 0.5

CTF amplitude correction was performed following 3D auto refinement in relion.

4C3I C1 6.9 FSC 0.143 CUT-OFF RELION 2.0 43843 RANDOM ASSIGNMENT RELION 2.0 PROJECTION MATCHING RELION 2.0 5 RELION 2.0 emd_8777.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 302.08 302.08 302.08 90.0 90.0 90.0 X Y Z -0.10179037 0.23072258 0.0028788708 0.015079218 2.36 2.36 2.36 0.07 AUTHOR ::::EMDATABANK.org::::EMD-8777:::: RNA polymerase I Initial Transcribing Complex with a truncated scaffold FLEXIBLE FIT REAL