2024-07-10 REL PDBe PDBe PDBe 2021-04-21 2021-12-08 2021-12-08 2024-07-10 Misiaszek AD Girbig M RNA polymerase I, human, rRNA transcription, DNA-dependent RNA polymerase, pre-initiation, Open Complex, TRANSCRIPTION Misiaszek AD Girbig M Grotsch H Baudin F Murciano B Lafita A Muller CW Nat.Struct.Mol.Biol. US 28 997 1008 2021 34887565 doi:10.1038/s41594-021-00693-4 1545-9985 7obb FULLOVERLAP RNA polymerase I Open Complex RNA polymerase I Open Complex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 0.60 RNA polymerase I 1 1 2 3 4 5 6 7 8 9 10 11 12 13 Homo sapiens DNA 1 14 15 Homo sapiens DNA-directed RNA polymerase I subunit RPA1 Homo sapiens 0.195069047 1 LEVO MLISKNMPWRRLQGISFGMYSAEELKKLSVKSITNPRYLDSLGNPSANGLYDLALGPADSKEVCSTCVQDFSNCSGHLGH IELPLTVYNPLLFDKLYLLLRGSCLNCHMLTCPRAVIHLLLCQLRVLEVGALQAVYELERILNRFLEENPDPSASEIREE LEQYTTEIVQNNLLGSQGAHVKNVCESKSKLIALFWKAHMNAKRCPHCKTGRSVVRKEHNSKLTITFPAMVHRTAGQKDS EPLGIEEAQIGKRGYLTPTSAREHLSALWKNEGFFLNYLFSGMDDDGMESRFNPSVFFLDFLVVPPSRYRPVSRLGDQMF TNGQTVNLQAVMKDVVLIRKLLALMAQEQKLPEEVATPTTDEEKDSLIAIDRSFLSTLPGQSLIDKLYNIWIRLQSHVNI VFDSEMDKLMMDKYPGIRQILEKKEGLFRKHMMGKRVDYAARSVICPDMYINTNEIGIPMVFATKLTYPQPVTPWNVQEL RQAVINGPNVHPGASMVINEDGSRTALSAVDMTQREAVAKQLLTPATGAPKPQGTKIVCRHVKNGDILLLNRQPTLHRPS IQAHRARILPEEKVLRLHYANCKAYNADFDGDEMNAHFPQSELGRAEAYVLACTDQQYLVPKDGQPLAGLIQDHMVSGAS MTTRGCFFTREHYMELVYRGLTDKVGRVKLLSPSILKPFPLWTGKQVVSTLLINIIPEDHIPLNLSGKAKITGKAWVKET PRSVPGFNPDSMCESQVIIREGELLCGVLDKAHYGSSAYGLVHCCYEIYGGETSGKVLTCLARLFTAYLQLYRGFTLGVE DILVKPKADVKRQRIIEESTHCGPQAVRAALNLPEAASYDEVRGKWQDAHLGKDQRDFNMIDLKFKEEVNHYSNEINKAC MPFGLHRQFPENSLQMMVQSGAKGSTVNTMQISCLLGQIELEGRRPPLMASGKSLPCFEPYEFTPRAGGFVTGRFLTGIK PPEFFFHCMAGREGLVDTAVKTSRSGYLQRCIIKHLEGLVVQYDLTVRDSDGSVVQFLYGEDGLDIPKTQFLQPKQFPFL ASNYEVIMKSQHLHEVLSRADPKKALHHFRAIKKWQSKHPNTLLRRGAFLSYSQKIQEAVKALKLESENRNGRSPGTQEM LRMWYELDEESRRKYQKKAAACPDPSLSVWRPDIYFASVSETFETKVDDYSQEWAAQTEKSYEKSELSLDRLRTLLQLKW QRSLCEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMVASANIKTPMMSVPVLNTKKALKRVKS LKKQLTRVCLGEVLQKIDVQESFCMEEKQNKFQVYQLRFQFLPHAYYQQEKCLRPEDILRFMETRFFKLLMESIKKKNNK ASAFRNVNTRRATQRDLDNAGELGRSRGEQEGDEEEEGHIVDAEAEEGDADASDAKRKEKQEEEVDYESEEEEEREGEEN DDEDMQEERNPHREGARKTQEQDEEVGLGTEEDPSLPALLTQPRKPTHSQEPQGPEAMERRVQAVREIHPFIDDYQYDTE ESLWCQVTVKLPLMKINFDMSSLVVSLAHGAVIYATKGITRCLLNETTNNKNEKELVLNTEGINLPELFKYAEVLDLRRL YSNDIHAIANTYGIEAALRVIEKEIKDVFAVYGIAVDPRHLSLVADYMCFEGVYKPLNRFGIRSNSSPLQQMTFETSFQF LKQATMLGSHDELRSPSACLVVGKVVRGGTGLFELKQPLR O95602 2.7.7.6 DNA-directed RNA polymerase I subunit RPA2 Homo sapiens 0.128379219 1 LEVO MDPGSRWRNLPSGPSLKHLTDPSYGIPREQQKAALQELTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFTILDA VISPPTVPKGTICKEANVYPAECRGRRSTYRGKLTADINWAVNGISKGIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHH EEAEEMGGYFIINGIEKVIRMLIMPRRNFPIAMIRPKWKTRGPGYTQYGVSMHCVREEHSAVNMNLHYLENGTVMLNFIY RKELFFLPLGFALKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNVPDWYPN EQAAEFLFNQCICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAF DKKAQKTSVSMNTDNLMRIFTMGIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFRCVHRGADFAK MRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGVTPIDGAPHRSYSECYPVLLDG VMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLALGKEELIGTMEQI FMNVAIFEDEVFAGVTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSP LVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGD PRVLQKLDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG DKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALE YFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEM ERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCSRSDTIDTVSVPYVFRYFV AELAAMNIKVKLDVV Q9H9Y6 2.7.7.6 DNA-directed RNA polymerases I and III subunit RPAC1 Homo sapiens 0.039301671999999996 1 LEVO MAASQAVEEMRSRVVLGEFGVRNVHTTDFPGNYSGYDDAWDQDRFEKNFRVDVVHMDENSLEFDMVGIDAAIANAFRRIL LAEVPTMAVEKVLVYNNTSIVQDEILAHRLGLIPIHADPRLFEYRNQGDEEGTEIDTLQFRLQVRCTRNPHAAKDSSDPN ELYVNHKVYTRHMTWIPLGNQADLFPEGTIRPVHDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFSPVATASYRLLPDIT LLEPVEGEAAEELSRCFSPGVIEVQEVQGKKVARVANPRLDTFSREIFRNEKLKKVVRLARVRDHYIFSVESTGVLPPDV LVSEAIKVLMGKCRRFLDELDAVQMD O15160 DNA-directed RNA polymerases I, II, and III subunit RPABC1 Homo sapiens 0.024644318 1 LEVO MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFPEEP KVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELL ARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLVQ P19388 DNA-directed RNA polymerases I, II, and III subunit RPABC2 Homo sapiens 0.014491025999999999 1 LEVO MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVM VELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD P61218 DNA-directed RNA polymerase I subunit RPA43 Homo sapiens 0.037490379 1 LEVO MAAGCSEAPRPAAASDGSLVGQAGVLPCLELPTYAAACALVNSRYSCLVAGPHQRHIALSPRYLNRKRTGIREQLDAELL RYSESLLGVPIAYDNIKVVGELGDIYDDQGHIHLNIEADFVIFCPEPGQKLMGIVNKVSSSHIGCLVHGCFNASIPKPEQ LSAEQWQTMEINMGDELEFEVFRLDSDAAGVFCIRGKLNITSLQFKRSEVSEEVTENGTEEAAKKPKKKKKKKDPETYEV DSGTTKLADDADDTPMEESALQNTNNANGIWEEEPKKKKKKKKHQEVQDQDPVFQGSDSSGYQSDHKKKKKKRKHSEEAE FTPPLKCSPKRKGKSNFL Q3B726 DNA-directed RNA polymerases I, II, and III subunit RPABC3 Homo sapiens 0.017162273 1 LEVO MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIASTLYEDGTLDDGEYNPTDD RPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLMRLQGDANNLHGFEVDSRVYLLMKKLAF P52434 DNA-directed RNA polymerase I subunit RPA12 Homo sapiens 0.013917694999999999 1 LEVO MSVMDLANTCSSFQSDLDFCSDCGSVLPLPGAQDTVTCIRCGFNINVRDFEGKVVKTSVVFHQLGTAMPMSVEEGPECQG PVVDRRCPRCGHEGMAYHTRQMRSADEGQTVFYTCTNCKFQEKEDS Q9P1U0 DNA-directed RNA polymerases I, II, and III subunit RPABC5 Homo sapiens 0.007655122999999999 1 LEVO MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLLNYAPLEK P62875 DNA-directed RNA polymerases I and III subunit RPAC2 Homo sapiens 0.015259222 1 LEVO MEEDQELERKISGLKTSMAEGERKTALEMVQAAGTDRHCVTFVLHEEDHTLGNSLRYMIMKNPEVEFCGYTTTHPSESKI NLRIQTRGTLPAVEPFQRGLNELMNVCQHVLDKFEASIKDYKDQKASRNESTF P0DPB6 DNA-directed RNA polymerases I, II, and III subunit RPABC4 Homo sapiens 0.007018243999999999 1 LEVO MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR P53803 DNA-directed RNA polymerase I subunit RPA49 Homo sapiens 0.04733023399999999 1 LEVO MAAEVLPSARWQYCGAPDGSQRAVLVQFSNGKLQSPGNMRFTLYENKDSTNPRKRNQRILAAETDRLSYVGNNFGTGALK CNTLCRHFVGILNKTSGQMEVYDAELFNMQPLFSDVSVESELALESQTKTYREKMDSCIEAFGTTKQKRALNTRRMNRVG NESLNRAVAKAAETIIDTKGVTALVSDAIHNDLQDDSLYLPPCYDDAAKPEDVYKFEDLLSPAEYEALQSPSEAFRNVTS EEILKMIEENSHCTFVIEALKSLPSDVESRDRQARCIWFLDTLIKFRAHRVVKRKSALGPGVPHIINTKLLKHFTCLTYN NGRLRNLISDSMKAKITAYVIILALHIHDFQIDLTVLQRDLKLSEKRMMEIAKAMRLKISKRRVSVAAGSEEDHKLGTLS LPLPPAQTSDRLAKRRKIT Q9GZS1 DNA-directed RNA polymerase I subunit RPA34 Homo sapiens 0.055065523 1 LEVO MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRY RVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTG PRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLE PLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEE AIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPE TEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEE MPGPPLNSESGEEAPTGRDKKRKQQQQQPV O15446 DNA template strand Homo sapiens 0.013274529 1 (DG)(DT)(DA)(DC)(DT)(DG)(DA)(DA)(DT)(DT)(DA)(DG)(DA)(DC)(DA)(DA)(DT)(DG)(DC)(DT) (DC)(DT)(DG)(DT)(DG)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DT)(DA)(DC)(DC)(DA)(DT)(DG)(DA) (DG)(DC)(DG) DNA DNA non-template strand Homo sapiens 0.013265516 1 (DC)(DG)(DC)(DT)(DC)(DA)(DT)(DG)(DG)(DT)(DA)(DC)(DT)(DA)(DG)(DG)(DC)(DT)(DT)(DC) (DG)(DG)(DA)(DG)(DA)(DA)(DG)(DT)(DT)(DG)(DT)(DC)(DT)(DA)(DA)(DT)(DT)(DC)(DA)(DG) (DT)(DA)(DC) DNA ZINC ION 6.5409e-05 7 ZN singleParticle particle 0.85 7.5 15.0 C8H18N2O4S HEPES 80.0 (NH4)2SO4 ammonium sulfate 5.0 MgCl2 magnesium chloride 10.0 C4H10O2S2 dithiothreitol Quantifoil R2/1 COPPER 200 PLASMA CLEANING 30 OTHER

NanoClean plasma cleaner (Fischione Instruments, Model 1070)

ETHANE 100 288 FEI VITROBOT MARK IV

blot force 3, blot time 0 s, wait time 0 s.

Human RNA polymerase I mixed in 1:1 molar ratio with RRN3 and in 1:1.5 molar ratio with DNA template

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.75 2.25 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 14224 41.2 1 2628144 C1 3.3 FSC 0.143 CUT-OFF RELION 3.1 175912 MAXIMUM LIKELIHOOD cryoSPARC 3.1 RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 2 200000.0 RELION 3.1

Masked classification was used at the final stages of processing

7AEI C PDB experimental model 7AEI E PDB experimental model 7AEI F PDB experimental model 7AEI H PDB experimental model 7AEI J PDB experimental model 7AEI K PDB experimental model 7AEI L PDB experimental model

Initial rigid body fitting with UCSF Chimera followed by manual model fitting in Coot.

emd_12797_msk_1.map emd_12797_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 236.73601 236.73601 236.73601 90.0 90.0 90.0 X Y Z -0.26558948 0.72398853 0.0068391347 0.034177158 0.822 0.822 0.822 AUTHOR ::::EMDATABANK.org::::EMD-12797:::: Human RNA Polymerase I Open Complex Map G, RELION masked classification on nucleic acids, sharpened with LocScale emd_12797_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 236.73601 236.73601 236.73601 90.0 90.0 90.0 X Y Z -0.0028978686 0.21228486 0.00046219438 0.0050476105 0.822 0.822 0.822 AUTHOR ::::EMDATABANK.org::::EMD-12797:::: Human RNA Polymerase I Open Complex Map G, RELION masked classification on nucleic acids, sharpened with LocalDeblur emd_12797_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 236.73601 236.73601 236.73601 90.0 90.0 90.0 X Y Z -0.008291779 0.02563786 0.00019507216 0.0015072145 0.822 0.822 0.822 AUTHOR ::::EMDATABANK.org::::EMD-12797:::: Human RNA Polymerase I Open Complex Map G, RELION masked classification on nucleic acids, unsharpened emd_12797_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 236.73601 236.73601 236.73601 90.0 90.0 90.0 X Y Z -0.002884552 0.20182931 0.00044272377 0.004803302 0.822 0.822 0.822 AUTHOR ::::EMDATABANK.org::::EMD-12797:::: Human RNA Polymerase I Open Complex Map F, sharpened with LocalDeblur emd_12797_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 236.73601 236.73601 236.73601 90.0 90.0 90.0 X Y Z -0.02450247 0.041521136 0.000196566 0.0034916014 0.822 0.822 0.822 AUTHOR ::::EMDATABANK.org::::EMD-12797:::: Human RNA Polymerase I Open Complex Map F, half-map 2 emd_12797_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 236.73601 236.73601 236.73601 90.0 90.0 90.0 X Y Z -0.02546468 0.04411791 0.00019643412 0.0034874496 0.822 0.822 0.822 AUTHOR ::::EMDATABANK.org::::EMD-12797:::: Human RNA Polymerase I Open Complex Map F, half-map 1