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- EMDB-11004: Structure of Mycobacterium smegmatis HelD protein in complex with... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11004 | |||||||||
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Title | Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State II, primary channel engaged and active site interfering | |||||||||
![]() | Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core (State 2) | |||||||||
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![]() | transcription cycle helicase-like protein RNA polymerase / trasncription / TRANSCRIPTION | |||||||||
Function / homology | ![]() DNA helicase complex / recombinational repair / 3'-5' DNA helicase activity / DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / hydrolase activity / response to antibiotic ...DNA helicase complex / recombinational repair / 3'-5' DNA helicase activity / DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / hydrolase activity / response to antibiotic / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.08 Å | |||||||||
![]() | Kouba T / Koval T | |||||||||
![]() | ![]() Title: Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase. Authors: Tomáš Kouba / Tomáš Koval' / Petra Sudzinová / Jiří Pospíšil / Barbora Brezovská / Jarmila Hnilicová / Hana Šanderová / Martina Janoušková / Michaela Šiková / Petr Halada / ...Authors: Tomáš Kouba / Tomáš Koval' / Petra Sudzinová / Jiří Pospíšil / Barbora Brezovská / Jarmila Hnilicová / Hana Šanderová / Martina Janoušková / Michaela Šiková / Petr Halada / Michal Sýkora / Ivan Barvík / Jiří Nováček / Mária Trundová / Jarmila Dušková / Tereza Skálová / URee Chon / Katsuhiko S Murakami / Jan Dohnálek / Libor Krásný / ![]() ![]() ![]() Abstract: RNA synthesis is central to life, and RNA polymerase (RNAP) depends on accessory factors for recovery from stalled states and adaptation to environmental changes. Here, we investigated the mechanism ...RNA synthesis is central to life, and RNA polymerase (RNAP) depends on accessory factors for recovery from stalled states and adaptation to environmental changes. Here, we investigated the mechanism by which a helicase-like factor HelD recycles RNAP. We report a cryo-EM structure of a complex between the Mycobacterium smegmatis RNAP and HelD. The crescent-shaped HelD simultaneously penetrates deep into two RNAP channels that are responsible for nucleic acids binding and substrate delivery to the active site, thereby locking RNAP in an inactive state. We show that HelD prevents non-specific interactions between RNAP and DNA and dissociates stalled transcription elongation complexes. The liberated RNAP can either stay dormant, sequestered by HelD, or upon HelD release, restart transcription. Our results provide insights into the architecture and regulation of the highly medically-relevant mycobacterial transcription machinery and define HelD as a clearing factor that releases RNAP from nonfunctional complexes with nucleic acids. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 84.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27.1 KB 27.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 111 KB | ||
Filedesc metadata | ![]() | 8.3 KB | ||
Others | ![]() ![]() ![]() | 166.7 MB 140.9 MB 140.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yysMC ![]() 6vsxC ![]() 6yxuC ![]() 6z11C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core (State 2) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8311 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Structure of Mycobacterium smegmatis HelD protein in complex...
File | emd_11004_additional_1.map | ||||||||||||
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Annotation | Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core (State 2) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Structure of Mycobacterium smegmatis HelD protein in complex...
File | emd_11004_half_map_1.map | ||||||||||||
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Annotation | Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core halfmap 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Structure of Mycobacterium smegmatis HelD protein in complex...
File | emd_11004_half_map_2.map | ||||||||||||
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Annotation | Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core (State 2) | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Mycobacterium smegmatis HelD protein in complex with RNA polymera...
Entire | Name: Mycobacterium smegmatis HelD protein in complex with RNA polymerase core (State 2) |
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Components |
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-Supramolecule #1: Mycobacterium smegmatis HelD protein in complex with RNA polymera...
Supramolecule | Name: Mycobacterium smegmatis HelD protein in complex with RNA polymerase core (State 2) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 444 KDa |
-Macromolecule #1: DNA-directed RNA polymerase subunit alpha
Macromolecule | Name: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 37.959441 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MLISQRPTLS EETVAENRSR FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTDIILNL KGLVVSSDD DEPVTMYLRK QGPGVVTAGD IVPPAGVTVH NPDMHIATLN DKGKLEVELV VERGRGYVPA VQNKASGAEI G RIPVDSIY ...String: MLISQRPTLS EETVAENRSR FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTDIILNL KGLVVSSDD DEPVTMYLRK QGPGVVTAGD IVPPAGVTVH NPDMHIATLN DKGKLEVELV VERGRGYVPA VQNKASGAEI G RIPVDSIY SPVLKVTYKV EATRVEQRTD FDKLIIDVET KNSISPRDAL ASAGGTLVEL FGLARELNAD SEHIEIGPSP AE ADHIASF ALPIDDLDLT VRSYNCLKRE GVHTVGELVA RTESDLLDIR NFGQKSIDEV KIKLHQLGLS LKDSPATFDP SEV AGYDAA TGTWTSDAGY DLDDNQDYAE TEQL UniProtKB: DNA-directed RNA polymerase subunit alpha |
-Macromolecule #2: DNA-directed RNA polymerase subunit beta
Macromolecule | Name: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 128.680141 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MLEGCILAVS SQSKSNAITN NSVPGAPNRV SFAKLREPLE VPGLLDVQTD SFEWLVGSDR WRQAAIDRGE ENPVGGLEEV LAELSPIED FSGSMSLSFS DPRFDEVKAS VDECKDKDMT YAAPLFVTAE FINNNTGEIK SQTVFMGDFP MMTEKGTFII N GTERVVVS ...String: MLEGCILAVS SQSKSNAITN NSVPGAPNRV SFAKLREPLE VPGLLDVQTD SFEWLVGSDR WRQAAIDRGE ENPVGGLEEV LAELSPIED FSGSMSLSFS DPRFDEVKAS VDECKDKDMT YAAPLFVTAE FINNNTGEIK SQTVFMGDFP MMTEKGTFII N GTERVVVS QLVRSPGVYF DETIDKSTEK TLHSVKVIPG RGAWLEFDVD KRDTVGVRID RKRRQPVTVL LKALGWTNEQ IV ERFGFSE IMMGTLEKDT TSGTDEALLD IYRKLRPGEP PTKESAQTLL ENLFFKEKRY DLARVGRYKV NKKLGLNAGK PIT SSTLTE EDVVATIEYL VRLHEGQTSM TVPGGVEVPV EVDDIDHFGN RRLRTVGELI QNQIRVGLSR MERVVRERMT TQDV EAITP QTLINIRPVV AAIKEFFGTS QLSQFMDQNN PLSGLTHKRR LSALGPGGLS RERAGLEVRD VHPSHYGRMC PIETP EGPN IGLIGSLSVY ARVNPFGFIE TPYRKVENGV VTDQIDYLTA DEEDRHVVAQ ANSPTDENGR FTEDRVMVRK KGGEVE FVS ADQVDYMDVS PRQMVSVATA MIPFLEHDDA NRALMGANMQ RQAVPLVRSE APLVGTGMEL RAAIDAGDVV VADKTGV IE EVSADYITVM ADDGTRQSYR LRKFARSNHG TCANQRPIVD AGQRVEAGQV IADGPCTQNG EMALGKNLLV AIMPWEGH N YEDAIILSNR LVEEDVLTSI HIEEHEIDAR DTKLGAEEIT RDIPNVSDEV LADLDERGIV RIGAEVRDGD ILVGKVTPK GETELTPEER LLRAIFGEKA REVRDTSLKV PHGESGKVIG IRVFSREDDD ELPAGVNELV RVYVAQKRKI SDGDKLAGRH GNKGVIGKI LPVEDMPFLP DGTPVDIILN THGVPRRMNI GQILETHLGW VAKAGWNIDV AAGVPDWASK LPEELYSAPA D STVATPVF DGAQEGELAG LLGSTLPNRD GEVMVDADGK STLFDGRSGE PFPYPVTVGY MYILKLHHLV DDKIHARSTG PY SMITQQP LGGKAQFGGQ RFGEMECWAM QAYGAAYTLQ ELLTIKSDDT VGRVKVYEAI VKGENIPEPG IPESFKVLLK ELQ SLCLNV EVLSSDGAAI EMRDGDDEDL ERAAANLGIN LSRNESASVE DLA UniProtKB: DNA-directed RNA polymerase subunit beta |
-Macromolecule #3: DNA-directed RNA polymerase subunit beta'
Macromolecule | Name: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 146.712891 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MLDVNFFDEL RIGLATADDI RNWSYGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRR ERMGHIELAA PVTHIWYFKG VPSRLGYLLD LAPKDLEKII YFAAYVITSV DDEMRHNELS TLEAEMAVEK K AVEDQRDA ...String: MLDVNFFDEL RIGLATADDI RNWSYGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRR ERMGHIELAA PVTHIWYFKG VPSRLGYLLD LAPKDLEKII YFAAYVITSV DDEMRHNELS TLEAEMAVEK K AVEDQRDA DLEARAQKLE ADLAELEAEG AKSDVRRKVR DSGEREMRQL RDRAQRELDR LDEIWNTFTK LAPKQLIVDE VL YRELQDR YGEYFTGAMG AESIKKLIEN FDIDAEAESL REVIRSGKGQ KKLRALKRLK VVAAFQQSGN SPMGMVLDAV PVI PPELRP MVQLDGGRFA TSDLNDLYRR VINRNNRLKR LIDLGAPEII VNNEKRMLQE SVDALFDNGR RGRPVTGPGN RPLK SLSDL LKGKQGRFRQ NLLGKRVDYS GRSVIVVGPQ LKLHQCGLPK LMALELFKPF VMKRLVDLNH AQNIKSAKRM VERQR PQVW DVLEEVIAEH PVLLNRAPTL HRLGIQAFEP QLVEGKAIQL HPLVCEAFNA DFDGDQMAVH LPLSAEAQAE ARILML SSN NILSPASGKP LAMPRLDMVT GLYYLTTLVE GATGEYQAAT KDAPEQGVYS SPAEAIMAMD RGALSVRAKI KVRLTEL RP PTDLEAQLFE NGWKPGDAWT AETTLGRVMF NELLPKSYPF VNEQMHKKVQ ARIINDLAER FPMIVVAQTV DKLKDAGF Y WATRSGVTVS MADVLVPPQK QEILERHEAE ADAIERKYQR GALNHTERNE SLVKIWQDAT EEVGKALEEF YPADNPIIT IVKSGATGNL TQTRTLAGMK GLVTNPKGEF IPRPIKSSFR EGLTVLEYFI NTHGARKGLA DTALRTADSG YLTRRLVDVS QDVIVREHD CETERGINVT LAERGPDGTL IRDAHVETSA FARTLATDAV DANGNVIIER GHDLGDPAID ALLAAGITTV K VRSVLTCT SATGVCAMCY GRSMATGKLV DIGEAVGIVA AQSIGEPGTQ LTMRTFHQGG VTGGADIVGG LPRVQELFEA RV PRNKAPI ADVAGRVRLE ESDKFFKITI VPDDGGEEVV YDKLSKRQRL RVITHEDGTE GVLSDGDHVE VGDQLMEGAA DPH EVLRVQ GPREVQIHLV KEVQEVYRAQ GVSIHDKHIE VIVRQMLRRV TIIDSGSTEF LPGSLTERAE FEAENRRVVA EGGE PAAGR PVLMGITKAS LATDSWLSAA SFQETTRVLT DAAINCRSDK LNGLKENVII GKLIPAGTGI SRYRNIQVQP TEEAR AAAY TIPSYEDQYY SPDFGQATGA AVPLDDYGYS DYR UniProtKB: DNA-directed RNA polymerase subunit beta' |
-Macromolecule #4: DNA-directed RNA polymerase subunit omega
Macromolecule | Name: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.544763 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSTPHADAQL NAADDLGIDS SAASAYDTPL GITNPPIDEL LSRASSKYAL VIYAAKRARQ INDYYNQLGD GILEYVGPLV EPGLQEKPL SIALREIHGD LLEHTEGE UniProtKB: DNA-directed RNA polymerase subunit omega |
-Macromolecule #5: RNA polymerase-associated transcription factor HelD
Macromolecule | Name: RNA polymerase-associated transcription factor HelD / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 81.298078 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSGRDYEDEL QSERDYVAGL YARLDAERAQ SQRRYAAALR EHGGTAVERD AEVRALAKDI ARLNVADNGL CFGRLDTLDD ARLYIGRLG IFDRDNDFEP LLLDWRAPMA RPFYVATAAN PENMRRRRQF HTLGRKVVDF TDEILGRPTG AEHDATNDAA L LAAVNAPR ...String: MSGRDYEDEL QSERDYVAGL YARLDAERAQ SQRRYAAALR EHGGTAVERD AEVRALAKDI ARLNVADNGL CFGRLDTLDD ARLYIGRLG IFDRDNDFEP LLLDWRAPMA RPFYVATAAN PENMRRRRQF HTLGRKVVDF TDEILGRPTG AEHDATNDAA L LAAVNAPR GEGMRDIVAT IQAEQDQVIR LDHTGVLVIE GGPGTGKTVV ALHRVAYLLY TYRKQMERHG VLVVGPTPAF LD HIGRVLP SLGESDAVFM TPGDFVPGLH VTAEDTPEAA EVKGSLKILD VLKAAVADRQ ELPSEPIPID LSDVTMRIDA ETA KWARDE ARKTGLPHNE ARAEFVDVVT YVVTERAVAR IGRGWLTRDD KHAWEKMRAD VVGELEDHEQ FNAALDALWP ILTP EDVLA QLYTSHERLR AAGAPECLWR ADGEAWTVSD VPLLDELVDL LGRNKAADEA AERERREEEA YAAGVLDLMV DREDL MDDE DHLLAQDLID AEELADRFKE QDNRELSERA AADREWTYGH VVVDEAQELS EMDWRLLMRR CPRRSFTIVG DLAQRR SPA GARSWGAMLD SYVPGRWVYK SLSVNYRTPA EIMAVAAAVL AEFAPDATPP DSVRACGVAP WARQVTDDDI ASAIAEF VS EEAGREGTSV VIGPPDVPGT VPPSETKGLE FDAVLVVEPE RILADGPRGA AELYVALTRA TQRLGVLYRD ALPQALAG L AEGDAAATVE QRTSA UniProtKB: Superfamily protein I DNA or RNA helicase |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #7: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: AB INITIO MODEL | ||||||
Output model | ![]() PDB-6yys: |