2025-04-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY database_2 em_admin _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update DATABASE_REFERENCES citation _citation.journal_volume _citation.page_first _citation.page_last STRUCTURE_SUMMARY pdbx_entry_details pdbx_molecule_features struct_ref _struct_ref.db_name _struct_ref.pdbx_db_accession DATABASE_REFERENCES em_admin pdbx_database_proc pdbx_seq_map_depositor_info struct_ref _em_admin.last_update _pdbx_seq_map_depositor_info.one_letter_code_mod _struct_ref.db_code OTHER atom_sites _atom_sites.fract_transf_matrix[1][1] _atom_sites.fract_transf_matrix[2][2] _atom_sites.fract_transf_matrix[3][3] STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_admin pdbx_entry_details pdbx_modification_feature _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update _pdbx_entry_details.has_protein_modification PDBe PDBe 2017-11-09 2017-12-20 2018-03-21 2025-04-09 European Research Council 693023 Germany German Research Foundation SFB860 Germany German Research Foundation SPP1935 Germany Liu X Farnung L Inhibitor, elongation, active site, TRANSCRIPTION Liu X Farnung L Wigge C Cramer P J. Biol. Chem. US 293 7189 7194 2018 29550768 doi:10.1074/jbc.RA118.002545 1083-351X 0071 JBCHA3 6exv FULLOVERLAP Mammalian RNA polymerase II elongation complex inhibited by Alpha-amanitin Mammalian RNA polymerase II elongation complex inhibited by Alpha-amanitin 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 0.607 RNA polymerase II elongation complex 1 1 2 3 4 5 6 7 8 9 10 11 12 Sus scrofa Thymus Nucleic acids 1 14 15 16 synthetic construct Alpha-amanitin 1 13 Amanita phalloides DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 Sus scrofa Thymus 0.217450078 1 LEVO MHGGGPPSGDSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTE CPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGEEM DNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEP RYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDN ELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNID RLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWS TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEV MNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGIL CKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKA HNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPF GFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVR NSINQVVQLRYGEDGLAGESVEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNAHIQNELEREFERMR EDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLL FNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLG VPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMP DFDVARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEEEEVVDKMD DDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKIIITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSN DIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLM EAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCKYGMEIPTNIPGLGAAGPTGMFFGSAPSPMGGISPAMTPW NQGATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPGYSPAWSPTPGSPGSPGPSSPYIPSPGGAMSPSYSPTSPAY EPRSPGGYTPQSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPNYTPTSP SYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSPTSPSYSPTSPSYSPSSPRYTPQSPTYTPSSPSYSPSSPSYSPTSPKYT PTSPSYSPSSPEYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTS PKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEEN I3LJR4 2.7.7.6 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 Sus scrofa Thymus 0.133201625 1 LEVO MQYDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEAQHASGEVEEPPRYLLK FEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTYCLLNGLT DRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTIWVSMLARGGQGA KKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGSRGAK PGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGM FKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNS PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKI FVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKERE YNNYSWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSA MGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFR SVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELEGTNRRY TKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIII NPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTY YQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAI ANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV I3LGP4 2.7.7.6 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 Sus scrofa Thymus 0.031439074 1 LEVO MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRLGLIPLTSDDIVD KLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELR LRAYAKKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN I3LCH3 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 Sus scrofa Thymus 0.016331255 1 LEVO MAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETI ASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQY A0A287ADR4 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 Sus scrofa Thymus 0.024644318 1 LEVO MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFPEEP KVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELL ARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLVQ I3LSI7 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 Sus scrofa Thymus 0.014477001 1 LEVO MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVM VELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIISD F1SKN8 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 Sus scrofa Thymus 0.019314282999999998 1 LEVO MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPF KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAI GSLMDDYLGLVS I3LJZ9 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 Sus scrofa Thymus 0.017162273 1 LEVO MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIASTLYEDGTLDDGEYNPTDD RPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLMRLQGDANNLHGFEVDSRVYLLMKKLAF I3LCB2 DNA-directed RNA polymerase II subunit RPB9 Sus scrofa Thymus 0.014541220999999998 1 LEVO MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITHEVDELTQIIADVSQDPTLPR TEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCGHRWTE P60899 DNA-directed RNA polymerases I, II, and III subunit RPABC5 Sus Scrofa Thymus 0.007655122999999999 1 LEVO MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLLNYAPLEK DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 Sus scrofa Thymus 0.013310283999999999 1 LEVO MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQTTPD YSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE F1RKE4 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 Sus scrofa Thymus 0.007018243999999999 1 LEVO MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR I3LN51 AMATOXIN Amanita phalloides 0.000939004 1 LEVO (ILX)(TRX)GIG(CSX)N(HYP) P85421 DNA (25-MER) synthetic construct 0.013303563 1 (DG)(DG)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DA)(DG)(DT)(DA)(DT)(DT)(DC)(DT)(DA)(DG)(DT) (DA)(DT)(DT)(DG)(DA)(DA)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DG)(DA)(DG)(DC)(DT)(DT)(DG) (DA)(DT)(DC) DNA RNA (5'-R(P*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3') synthetic construct 0.006414902 1 UAUAUGCAUAAAGACCAGGC DNA (36-MER) synthetic construct 0.013178483 1 (DG)(DA)(DT)(DC)(DA)(DA)(DG)(DC)(DT)(DC)(DA)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DA)(DA) (DG)(DC)(DC)(DT)(DG)(DG)(DT)(DC)(DT)(DA)(DT)(DA)(DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT) (DG)(DC)(DC) DNA ZINC ION 6.5409e-05 8 ZN MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 0.244 7.6 Quantifoil R2/2 GOLD 300 GLOW DISCHARGE 45 AIR ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.5 2.5 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 10.0 GIF Quantum LS 0 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3838 1 2264 10.0 35.0 1 207410 EMD-3219 C1 3.6 FSC 0.143 CUT-OFF RELION 134512 PROJECTION MATCHING 1 7.5 RELION PROJECTION MATCHING 1 1.8 RELION FLEXIBLE FIT REAL 53.969999999999999 emd_3981_msk_1.map emd_3981_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.92 273.92 273.92 90.0 90.0 90.0 X Y Z -0.028367093 0.05924922 -0.00010533071 0.0031144242 1.07 1.07 1.07 AUTHOR ::::EMDATABANK.org::::D_1200007408:::: Half-map post-refinement of mammalian RNA polymerase II elongation complex inhibited by %u03B1-amanitin emd_3981_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.92 273.92 273.92 90.0 90.0 90.0 X Y Z -0.028367093 0.05924922 -0.00010533071 0.0031144242 1.07 1.07 1.07 AUTHOR ::::EMDATABANK.org::::D_1200007408:::: Half-map post-refinement of mammalian RNA polymerase II elongation complex inhibited by %u03B1-amanitin