2024-05-22 REL PDBe PDBe PDBe 2019-12-14 2020-03-18 2020-03-18 2024-05-22 German Research Foundation (DFG) EN 1204/1-1 Germany German Research Foundation (DFG) CRC 960 Germany Pilsl M Engel C Transcription Initiation, Ribosome Biosynthesis, RNA Polymerase I, TRANSCRIPTION Pilsl M Engel C Nat Commun UK 11 1206 1206 2020 32139698 doi:10.1038/s41467-020-15052-y 2041-1723 6tps FULLOVERLAP early intermediate RNA-Polymerase I Pre-initiation Complex - eiPIC early intermediate RNA-Polymerase I Pre-initiation Complex - eiPIC 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 RNA polymerase 1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Saccharomyces cerevisiae transcription initiation factor 1 15 16 17 18 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) DNA 1 19 20 21 22 Synthetic construct DNA-directed RNA polymerase I subunit RPA190 Saccharomyces cerevisiae 0.186676969

(.ZN)(.ZN)(.MG)

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 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 0.037732613 1 LEVO MSNIVGIEYNRVTNTTSTDFPGFSKDAENEWNVEKFKKDFEVNISSLDAREANFDLINIDTSIANAFRRIMISEVPSVAA EYVYFFNNTSVIQDEVLAHRIGLVPLKVDPDMLTWVDSNLPDDEKFTDENTIVLSLNVKCTRNPDAPKGSTDPKELYNNA HVYARDLKFEPQGRQSTTFADCPVVPADPDILLAKLRPGQEISLKAHCILGIGGDHAKFSPVSTASYRLLPQINILQPIK GESARRFQKCFPPGVIGIDEGSDEAYVKDARKDTVSREVLRYEEFADKVKLGRVRNHFIFNVESAGAMTPEEIFFKSVRI LKNKAEYLKNCPITQ P07703 DNA-directed RNA polymerase I subunit RPA14 Saccharomyces cerevisiae 0.014599128 1 LEVO MMKGSRRTGNNTATTLNTPVVIHATQLPQHVSTDEVLQFLESFIDEKENIIDSTTMNTISGNAADADAAAVANTSLNIDT NLSSSISQLKRIQRDFKGLPPAQDFSAAPIQVSTTEKKETSIGVSATGGKKTTFADE P50106 DNA-directed RNA polymerases I, II, and III subunit RPABC1 Saccharomyces cerevisiae 0.025117094 1 LEVO MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWV EFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDE KRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM P20434 DNA-directed RNA polymerases I, II, and III subunit RPABC2 Saccharomyces cerevisiae 0.017931833999999997 1 LEVO MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRA TTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL P20435 DNA-directed RNA polymerase I subunit RPA43 Saccharomyces cerevisiae 0.036264852 1 LEVO MSQVKRANENRETARFIKKHKKQVTNPIDEKNGTSNCIVRVPIALYVSLAPMYLENPLQGVMKQHLNPLVMKYNNKVGGV VLGYEGLKILDADPLSKEDTSEKLIKITPDTPFGFTWCHVNLYVWQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKN NIPVDWTFVHNDVEEDADVINTDENNGNNNNEDNKDSNGGSNSLGKFSFGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTG RVVSVDGTLISDADEEGNGYNSSRSQAESLPIVSNKKIVFDDEVSIENKESHKELDLPEVKEDNGSEIVYEENTSESNDG ESSDSD P46669 DNA-directed RNA polymerases I, II, and III subunit RPABC3 Saccharomyces cerevisiae 0.016525363 1 LEVO MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWR PPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR P20436 DNA-directed RNA polymerase I subunit RPA12 Saccharomyces cerevisiae 0.013676566 1 LEVO MSVVGSLIFCLDCGDLLENPNAVLGSNVECSQCKAIYPKSQFSNLKVVTTTADDAFPSSLRAKKSVVKTSLKKNELKDGA TIKEKCPQCGNEEMNYHTLQLRSADEGATVFYTCTSCGYKFRTNN P32529 DNA-directed RNA polymerases I, II, and III subunit RPABC5 Saccharomyces cerevisiae 0.008290732 1 LEVO MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD P22139 DNA-directed RNA polymerases I and III subunit RPAC2 Saccharomyces cerevisiae 0.01616786 1 LEVO MTEDIEQKKTATEVTPQEPKHIQEEEEQDVDMTGDEEQEEEPDREKIKLLTQATSEDGTSASFQIVEEDHTLGNALRYVI MKNPDVEFCGYSIPHPSENLLNIRIQTYGETTAVDALQKGLKDLMDLCDVVESKFTEKIKSM P28000 DNA-directed RNA polymerases I, II, and III subunit RPABC4 Saccharomyces cerevisiae 0.007729969 1 LEVO MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR P40422 DNA-directed RNA polymerase I subunit RPA49 Saccharomyces cerevisiae 0.046721707 1 LEVO MSVKRSVSEIEIESVQDQPSVAVGSFFKGFRAPSDTTFDLYKKKKSEKDEFVLHGENERLEYEGYTDSSSQASNQYVVGL FNPEKKSIQLYKAPVLVSKVVSKSSKNLRGPKIKSKSDTRPSALRNALGEAFGTKKAKKAIADLERNRIDSDKLTDSAID IVDSVRTASKDLPTRAQLDEITSNDRPTPLANIDATDVEQIYPIESIIPKKELQFIRVSSILKEADKEKKLELFPYQNNS KYVAKKLDSLTQPSQMTKLQLLYYLSLLLGVYENRRVNNKTKLLERLNSPPEILVDGILSRFTVIKPGQFGRSKDRSYFI DPQNEDKILCYILAIIMHLDNFIVEITPLAHELNLKPSKVVSLFRVLGAIVKGATVAQAEAFGIPKSTAASYKIATMKVP FKLPEMTRRGRGPRR Q01080 DNA-directed RNA polymerase I subunit RPA34 Saccharomyces cerevisiae 0.026933518 1 LEVO MSKLSKDYVSDSDSDDEVISNEFSIPDGFKKCKHLKNFPLNGDNKKKAKQQQVWLIKFPSNVDISKLKSLPVDFESSTTM TIDKHDYKIMDDTDIESSLTQDNLSNMTLLVPSESKESLKIASTAKDNAPLQFDKVFSVSETAKIPAIDYSKVRVPRKDV PKVEGLKLEHFATGYDAEDFHVAEEVKENKKEPKKRSHHDDEEESSEKKKKKKEKREKREKKDKKDKKKKHRD P47006 RNA polymerase I-specific transcription initiation factor RRN3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.072458258 1 Escherichia coli LEVO MMAFENTSKRPPQDFVAPIDQKKRKVQFSDSTGLVTLQPEEIKDEVFSAAMYSRFVKSALDDLDKNDSTQIGIIANQVAL PSKNPERINDKNLNILLDILSSNINRIESSRGTFLIQSIINFEKWWELPPHTLSKYIYFIKILCSSIPKWWQDVSMILVS CFILPIKQTVCHHDMLKYFLRMIPSSMGFIDTYLAKFFPNKNDTRRKLVNYTSNLLKLRGYCSELGFQIWSLLIEKIISI DVELQNELDELDDDVDDDDLEEVDLEDDDDLDDDSGDDDDENCGNSNEELRSGAADGSQSDSEDMDIIEGMDGTEEYNVE LTQGIKELSTKLDSILTLVSTHVEEQVTPESLESGEGVGVFNTLTTLFKTHVLPTYYTRSIQYIMFHVSQQQLELMDSFL VTLIDISFAVNEAAEKKIKSLQYLGSYIARAKKLSRTQIIFVASYLTSWLNRYVIEREEEVDQRGGMERFKHFYAAFQAL CYIFCFRHNIFRDTDGNWECELDKFFQRMVISKFNPLKFCNENVMLMFARIAQQESVAYCFSIIENNNNERLRGIIGKAD SDKKENSAQANTTSSSWSLATRQQFIDLQSYFPYDPLFLKNYKILMKEYYIEWSEASGEYESDGSDD P36070 RNA polymerase I-specific transcription initiation factor RRN6 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.073523516 1 Escherichia coli LEVO RPVDDTLAEDALDLHIVVKSLLCDTQDAFFWDPTVANRLDSQYIQTASDLRNYRDGTEIIAYASGKTGSVLNIAVLTRQN TLHLNRHNNVTSIELHSPIKSIKIPGASESIGRRSNLVGIITENSFQIFRIESVHSRSCDVMVSSSEPLYFVEIDDLQVV DFAFNPWDLQQFAIIDIKGNWSIGRIPKNFNNNNKRKLQLIDNLHGTIFDPEELSSWKRIEWFSHFQKILVFDRSKMIEI DFMNNWQTEVVQAKAWSNIRDYKRIDDKNGILLTSREIIIVGASESNDPVRRISWKHDLDPDDTTLRITVQKVKKPDHIL LVAFVYSMRHKRIYMHVFSHRKANLFQSLGCSTVLEIPGGTPTGIETILTLDHIDDESRREEDADENFELVVDFLVKLRN SSEVYYYALSNTQNSEPNKQETPIIVDHPEWASLFNNADEREKESIGALVSQIKLKERERISRVQNLIEHENSHDEDKYL QDLGYRLSIATNELLESWQKTKDESILSGSLSHSKLKNLLENSDSFASIPEFSSLLDQFFQYYQDQDVTFIGFEKLLHLF LHEDVPGLDIFYNKLLQCWVLVSPQAELLTKEIVKDIIWSLARLEKPSLFEPIQNEISRSLSGPYQDIISSWDMDD P32786 RNA polymerase I-specific transcription initiation factor RRN7 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.060435195 1 Escherichia coli LEVO MSTFIRGPICGTDNCPSRLWRIIDGRRTCQYGHVMEGDVEFNDDEDDLNGLGAGVITRRLNLTTNATGSFQSSQLTNSQL LQQQQRQSHKKFKKLIGHEAKLLFLKSFQFILKRQIRWLITEMRFPKEFEHVAKIIWLKILKTINDQPQEELKLQLHMTS TISILYLASTHLSLPVYTCDYIKWICTAKMPYFQASEILPKSWRIQLPNYYVSILEGSISPFNGQLYNKIALTCGMIHFK EFFNSEISCQGLLLKLVMQCALPPEFYFYTKQVIEFEETDIRNLTLWERTDERHTGRVSNHAELRVLSYFMLTINWMLSF DRDRQYPLKWILSLTESLTQRTTTSESIGRNIVKVVYPDKPTSSDYFQWSEEETLEFLKWMEKQFLPTQTKSLHNENGSM EMTIDQKIARRKLYKIFPLDREANHDGEFNDSTHQLTFIEDLQERYAKQTPFFESNKIRDSLNYQEANPPARKEAIGRLL THIASQLLVDFAISKEQLKDCISRIKNACLHRMN P40992 RNA polymerase I-specific transcription initiation factor RRN11 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.059334262 1 Escherichia coli LEVO MFEVPITLTNRKFAQRRKLKYQYINYISRRFDRISKKSTTTDSLPTPENSAAENNDEEEGQNSEAGTYRRSVLQQKKRRR ERHWRSVVGEIYSTTESETDSQEEETEEGGEHDTGIDKEDSDEERKFWKKYEKPEKSFEIWRTVSSQNKQPINKQKMTYH NFKKIEKIPLRKMEIPLLHCTKENKLYFQSISRGLEPLKTSTSEVRNYRTRHIVTLTDLLHLNVSRHNWSLAYKIFATLI RIPGVQIKSLWGIGVEILDNLSNSSSGLDFLQWMCQIYSSKSRFVQNINYRSIVPPFQTGSRTHTAKFAITYLWSSLINC QKSMEPSSNIIDKPFDTENDLLQELIDKISEWVLTPPFMEDAEVWFIYASCHLLKADTLSRQFVNDNKNNDLIGLDRDIK INQVIKHIHYVRTFLKICLDKGGFAVPSRLIENQLKSFESRLYGEAQDIQERDVANVYDSIDNSSVENSFGDVYETNAEF LDTQLMDLSPEDNGLDEMHYSDEDSSE Q04712 NTS-DNA (27-MER) Synthetic construct 0.008411627 1 (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA) DNA TS-DNA (27-MER) Synthetic construct 0.008153236 1 (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT) DNA DNA foreign Synthetic construct 0.003905512 1 (DG)(DG)(DG)(DG)(DG)(DG)(DG)(DG)(DG)(DG)(DG)(DG) DNA DNA foreign Synthetic construct 0.003425224 1 (DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC) DNA ZINC ION 6.5409e-05 7 ZN MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 0.1 7.8 KCl Quantifoil R2/1 COPPER 300 CARBON CONTINUOUS 0.2 PLASMA CLEANING 60 OTHER ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.01 1.5 3.5 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 1 4088 1.4 1

Initial model generated from 2D classes

1 C1 3.54 FSC 0.143 CUT-OFF RELION 3.08 122099 ANGULAR RECONSTITUTION RELION 3.0 ANGULAR RECONSTITUTION RELION 3.0 emd_10544_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 0 0 0 420 420 420 457.80002 457.80002 457.80002 90.0 90.0 90.0 X Y Z -0.030239038 0.05790723 -0.000033872384 0.0013648649 1.09 1.09 1.09 AUTHOR ::::EMDATABANK.org::::EMD-10544:::: focused CF refinement postporocessed