2021-09-29RELPDBePDBePDBe2020-05-052020-11-042020-11-042021-09-29Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State II, primary channel engaged and active site interferingKouba TKoval TKrasny LDohnalek JKouba TKoval' TSudzinova PPospisil JBrezovska BHnilicova JSanderova HJanouskova MSikova MHalada PSykora MBarvik INovacek JTrundova MDuskova JSkalova TChon UMurakami KSDohnalek JKrasny LMycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase.Nat CommunUK1164196419202033339823doi:10.1038/s41467-020-20158-42041-1723EMD-10996other EM volumeEMD-11004associated EM volumeStructure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core (State 2)6yysFULLOVERLAPMycobacterium smegmatis HelD protein in complex with RNA polymerase core (State 2)Mycobacterium smegmatis HelD protein in complex with RNA polymerase core (State 2)012345Mycolicibacterium smegmatis MC2 155Escherichia coli0.444DNA-directed RNA polymerase subunit alphaMycolicibacterium smegmatis MC2 1550.0379594412Escherichia coliLEVOMLISQRPTLSEETVAENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDIILNL
KGLVVSSDDDEPVTMYLRKQGPGVVTAGDIVPPAGVTVHNPDMHIATLNDKGKLEVELVVERGRGYVPAVQNKASGAEIG
RIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLIIDVETKNSISPRDALASAGGTLVELFGLARELNADSEHIEIGPSPAE
ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPATFDPSEV
AGYDAATGTWTSDAGYDLDDNQDYAETEQL2.7.7.6DNA-directed RNA polymerase subunit betaMycolicibacterium smegmatis MC2 1550.1286801411Escherichia coliLEVOMLEGCILAVSSQSKSNAITNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLVGSDRWRQAAIDRGEENPVGGLEEV
LAELSPIEDFSGSMSLSFSDPRFDEVKASVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIIN
GTERVVVSQLVRSPGVYFDETIDKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV
ERFGFSEIMMGTLEKDTTSGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLNAGKPIT
SSTLTEEDVVATIEYLVRLHEGQTSMTVPGGVEVPVEVDDIDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDV
EAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETP
EGPNIGLIGSLSVYARVNPFGFIETPYRKVENGVVTDQIDYLTADEEDRHVVAQANSPTDENGRFTEDRVMVRKKGGEVE
FVSADQVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVADKTGV
IEEVSADYITVMADDGTRQSYRLRKFARSNHGTCANQRPIVDAGQRVEAGQVIADGPCTQNGEMALGKNLLVAIMPWEGH
NYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPK
GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRH
GNKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAKAGWNIDVAAGVPDWASKLPEELYSAPAD
STVATPVFDGAQEGELAGLLGSTLPNRDGEVMVDADGKSTLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPY
SMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQ
SLCLNVEVLSSDGAAIEMRDGDDEDLERAAANLGINLSRNESASVEDLA2.7.7.6DNA-directed RNA polymerase subunit beta'Mycolicibacterium smegmatis MC2 1550.146712890999999981Escherichia coliLEVOMLDVNFFDELRIGLATADDIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGV
EVTRAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDDEMRHNELSTLEAEMAVEKK
AVEDQRDADLEARAQKLEADLAELEAEGAKSDVRRKVRDSGEREMRQLRDRAQRELDRLDEIWNTFTKLAPKQLIVDEVL
YRELQDRYGEYFTGAMGAESIKKLIENFDIDAEAESLREVIRSGKGQKKLRALKRLKVVAAFQQSGNSPMGMVLDAVPVI
PPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLK
SLSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQR
PQVWDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPQLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARILML
SSNNILSPASGKPLAMPRLDMVTGLYYLTTLVEGATGEYQAATKDAPEQGVYSSPAEAIMAMDRGALSVRAKIKVRLTEL
RPPTDLEAQLFENGWKPGDAWTAETTLGRVMFNELLPKSYPFVNEQMHKKVQARIINDLAERFPMIVVAQTVDKLKDAGF
YWATRSGVTVSMADVLVPPQKQEILERHEAEADAIERKYQRGALNHTERNESLVKIWQDATEEVGKALEEFYPADNPIIT
IVKSGATGNLTQTRTLAGMKGLVTNPKGEFIPRPIKSSFREGLTVLEYFINTHGARKGLADTALRTADSGYLTRRLVDVS
QDVIVREHDCETERGINVTLAERGPDGTLIRDAHVETSAFARTLATDAVDANGNVIIERGHDLGDPAIDALLAAGITTVK
VRSVLTCTSATGVCAMCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTQLTMRTFHQGGVTGGADIVGGLPRVQELFEARV
PRNKAPIADVAGRVRLEESDKFFKITIVPDDGGEEVVYDKLSKRQRLRVITHEDGTEGVLSDGDHVEVGDQLMEGAADPH
EVLRVQGPREVQIHLVKEVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIIDSGSTEFLPGSLTERAEFEAENRRVVAEGGE
PAAGRPVLMGITKASLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGISRYRNIQVQPTEEAR
AAAYTIPSYEDQYYSPDFGQATGAAVPLDDYGYSDYR2.7.7.6DNA-directed RNA polymerase subunit omegaMycolicibacterium smegmatis MC2 1550.0115447631Escherichia coliLEVOMSTPHADAQLNAADDLGIDSSAASAYDTPLGITNPPIDELLSRASSKYALVIYAAKRARQINDYYNQLGDGILEYVGPLV
EPGLQEKPLSIALREIHGDLLEHTEGE2.7.7.6RNA polymerase-associated transcription factor HelDMycolicibacterium smegmatis MC2 1550.0812980781Escherichia coliLEVOMSGRDYEDELQSERDYVAGLYARLDAERAQSQRRYAAALREHGGTAVERDAEVRALAKDIARLNVADNGLCFGRLDTLDD
ARLYIGRLGIFDRDNDFEPLLLDWRAPMARPFYVATAANPENMRRRRQFHTLGRKVVDFTDEILGRPTGAEHDATNDAAL
LAAVNAPRGEGMRDIVATIQAEQDQVIRLDHTGVLVIEGGPGTGKTVVALHRVAYLLYTYRKQMERHGVLVVGPTPAFLD
HIGRVLPSLGESDAVFMTPGDFVPGLHVTAEDTPEAAEVKGSLKILDVLKAAVADRQELPSEPIPIDLSDVTMRIDAETA
KWARDEARKTGLPHNEARAEFVDVVTYVVTERAVARIGRGWLTRDDKHAWEKMRADVVGELEDHEQFNAALDALWPILTP
EDVLAQLYTSHERLRAAGAPECLWRADGEAWTVSDVPLLDELVDLLGRNKAADEAAERERREEEAYAAGVLDLMVDREDL
MDDEDHLLAQDLIDAEELADRFKEQDNRELSERAAADREWTYGHVVVDEAQELSEMDWRLLMRRCPRRSFTIVGDLAQRR
SPAGARSWGAMLDSYVPGRWVYKSLSVNYRTPAEIMAVAAAVLAEFAPDATPPDSVRACGVAPWARQVTDDDIASAIAEF
VSEEAGREGTSVVIGPPDVPGTVPPSETKGLEFDAVLVVEPERILADGPRGAAELYVALTRATQRLGVLYRDALPQALAG
LAEGDAAATVEQRTSA3.6.4.12ZINC ION6.5409e-052ZNMAGNESIUM ION2.4305e-051MGsingleParticleparticle7.8ETHANEFEI VITROBOT MARK IVFEI TITAN KRIOSFLOOD BEAMBRIGHT FIELDFIELD EMISSION GUN300GATAN K2 SUMMIT (4k x 4k)COUNTING50.01RELION6F6WC13.08FSC 0.143 CUT-OFFRELION3.1173500MAXIMUM LIKELIHOODMAXIMUM LIKELIHOODRELIONRELION6F6W6VSXAB INITIO MODELemd_11004_additional_1.map.gz1IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
360
360360
0
00360360360299.19598299.19598299.1959890.090.090.0XYZ-0.0673134550.112662487.969672e-050.0040292480.83109990.83109990.8310999Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core (State 2)emd_11004_half_map_1.map.gz1IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
360
360360
0
00360360360299.19598299.19598299.1959890.090.090.0XYZ-0.0242645240.045255917.9870464e-050.00244344440.83109990.83109990.8310999Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core halfmap 1emd_11004_half_map_2.map.gz1IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
360
360360
0
00360360360299.19598299.19598299.1959890.090.090.0XYZ-0.0238943660.0471945447.952297e-050.00243130950.83109990.83109990.8310999Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core (State 2)