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Yorodumi- EMDB-14696: Protomeric substructure from an octameric assembly of M. tubercul... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14696 | ||||||||||||
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Title | Protomeric substructure from an octameric assembly of M. tuberculosis RNA polymerase in complex with sigma-b initiation factor | ||||||||||||
Map data | sharpened map | ||||||||||||
Sample |
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Keywords | RNA polymerase / self-assembly / octamer / tuberculosis / stress response / hibernation / TRANSCRIPTION | ||||||||||||
Function / homology | Function and homology information Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / peptidoglycan-based cell wall / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic ...Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / peptidoglycan-based cell wall / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.86 Å | ||||||||||||
Authors | Trapani S / Bron P / Lai Kee Him J / Brodolin K / Morichaud Z / Vishwakarma R | ||||||||||||
Funding support | France, 3 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization. Authors: Zakia Morichaud / Stefano Trapani / Rishi K Vishwakarma / Laurent Chaloin / Corinne Lionne / Joséphine Lai-Kee-Him / Patrick Bron / Konstantin Brodolin / Abstract: Self-assembly of macromolecules into higher-order symmetric structures is fundamental for the regulation of biological processes. Higher-order symmetric structure self-assembly by the gene expression ...Self-assembly of macromolecules into higher-order symmetric structures is fundamental for the regulation of biological processes. Higher-order symmetric structure self-assembly by the gene expression machinery, such as bacterial DNA-dependent RNA polymerase (RNAP), has never been reported before. Here, we show that the stress-response σ factor from the human pathogen, Mycobacterium tuberculosis, induces the RNAP holoenzyme oligomerization into a supramolecular complex composed of eight RNAP units. Cryo-electron microscopy revealed a pseudo-symmetric structure of the RNAP octamer in which RNAP protomers are captured in an auto-inhibited state and display an open-clamp conformation. The structure shows that σ is sequestered by the RNAP flap and clamp domains. The transcriptional activator RbpA prevented octamer formation by promoting the initiation-competent RNAP conformation. Our results reveal that a non-conserved region of σ is an allosteric controller of transcription initiation and demonstrate how basal transcription factors can regulate gene expression by modulating the RNAP holoenzyme assembly and hibernation. #1: Journal: Biorxiv / Year: 2022 Title: Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization Authors: Morichaud Z / Trapani S / Vishwakarma R / Chaloin L / Lionne C / Lai-Kee-Him J / Bron P / Brodolin K | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14696.map.gz | 227 MB | EMDB map data format | |
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Header (meta data) | emd-14696-v30.xml emd-14696.xml | 32 KB 32 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14696_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_14696.png | 112.9 KB | ||
Filedesc metadata | emd-14696.cif.gz | 8.8 KB | ||
Others | emd_14696_additional_1.map.gz emd_14696_additional_2.map.gz emd_14696_half_map_1.map.gz emd_14696_half_map_2.map.gz | 189.7 MB 219.8 MB 192.9 MB 192.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14696 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14696 | HTTPS FTP |
-Related structure data
Related structure data | 7zf2MC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14696.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: unsharpened map
File | emd_14696_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: octameric assembly of (alpha,alpha,beta,beta',omega,sigma-b) protomers....
File | emd_14696_additional_2.map | ||||||||||||
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Annotation | octameric assembly of (alpha,alpha,beta,beta',omega,sigma-b) protomers. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14696_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14696_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : M. tuberculosis RNA polymerase in complex with sigma-b initiation...
Entire | Name: M. tuberculosis RNA polymerase in complex with sigma-b initiation factor |
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Components |
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-Supramolecule #1: M. tuberculosis RNA polymerase in complex with sigma-b initiation...
Supramolecule | Name: M. tuberculosis RNA polymerase in complex with sigma-b initiation factor type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
Molecular weight | Theoretical: 101 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: Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv |
Molecular weight | Theoretical: 37.745328 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MLISQRPTLS EDVLTDNRSQ FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTEIILNL KSLVVSSEE DEPVTMYLRK QGPGEVTAGD IVPPAGVTVH NPGMHIATLN DKGKLEVELV VERGRGYVPA VQNRASGAEI G RIPVDSIY ...String: MLISQRPTLS EDVLTDNRSQ FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTEIILNL KSLVVSSEE DEPVTMYLRK QGPGEVTAGD IVPPAGVTVH NPGMHIATLN DKGKLEVELV VERGRGYVPA VQNRASGAEI G RIPVDSIY SPVLKVTYKV DATRVEQRTD FDKLILDVET KNSISPRDAL ASAGKTLVEL FGLARELNVE AEGIEIGPSP AE ADHIASF ALPIDDLDLT VRSYNCLKRE GVHTVGELVA RTESDLLDIR NFGQKSIDEV KIKLHQLGLS LKDSPPSFDP SEV AGYDVA TGTWSTEGAY DEQDYAETEQ L 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: Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv |
Molecular weight | Theoretical: 129.602344 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MVLADSRQSK TAASPSPSRP QSSSNNSVPG APNRVSFAKL REPLEVPGLL DVQTDSFEWL IGSPRWRESA AERGDVNPVG GLEEVLYEL SPIEDFSGSM SLSFSDPRFD DVKAPVDECK DKDMTYAAPL FVTAEFINNN TGEIKSQTVF MGDFPMMTEK G TFIINGTE ...String: MVLADSRQSK TAASPSPSRP QSSSNNSVPG APNRVSFAKL REPLEVPGLL DVQTDSFEWL IGSPRWRESA AERGDVNPVG GLEEVLYEL SPIEDFSGSM SLSFSDPRFD DVKAPVDECK DKDMTYAAPL FVTAEFINNN TGEIKSQTVF MGDFPMMTEK G TFIINGTE RVVVSQLVRS PGVYFDETID KSTDKTLHSV KVIPSRGAWL EFDVDKRDTV GVRIDRKRRQ PVTVLLKALG WT SEQIVER FGFSEIMRST LEKDNTVGTD EALLDIYRKL RPGEPPTKES AQTLLENLFF KEKRYDLARV GRYKVNKKLG LHV GEPITS STLTEEDVVA TIEYLVRLHE GQTTMTVPGG VEVPVETDDI DHFGNRRLRT VGELIQNQIR VGMSRMERVV RERM TTQDV EAITPQTLIN IRPVVAAIKE FFGTSQLSQF MDQNNPLSGL THKRRLSALG PGGLSRERAG LEVRDVHPSH YGRMC PIET PEGPNIGLIG SLSVYARVNP FGFIETPYRK VVDGVVSDEI VYLTADEEDR HVVAQANSPI DADGRFVEPR VLVRRK AGE VEYVPSSEVD YMDVSPRQMV SVATAMIPFL EHDDANRALM GANMQRQAVP LVRSEAPLVG TGMELRAAID AGDVVVA EE SGVIEEVSAD YITVMHDNGT RRTYRMRKFA RSNHGTCANQ CPIVDAGDRV EAGQVIADGP CTDDGEMALG KNLLVAIM P WEGHNYEDAI ILSNRLVEED VLTSIHIEEH EIDARDTKLG AEEITRDIPN ISDEVLADLD ERGIVRIGAE VRDGDILVG KVTPKGETEL TPEERLLRAI FGEKAREVRD TSLKVPHGES GKVIGIRVFS REDEDELPAG VNELVRVYVA QKRKISDGDK LAGRHGNKG VIGKILPVED MPFLADGTPV DIILNTHGVP RRMNIGQILE THLGWCAHSG WKVDAAKGVP DWAARLPDEL L EAQPNAIV STPVFDGAQE AELQGLLSCT LPNRDGDVLV DADGKAMLFD GRSGEPFPYP VTVGYMYIMK LHHLVDDKIH AR STGPYSM ITQQPLGGKA QFGGQRFGEM ECWAMQAYGA AYTLQELLTI KSDDTVGRVK VYEAIVKGEN IPEPGIPESF KVL LKELQS LCLNVEVLSS DGAAIELREG EDEDLERAAA NLGINLSRNE SASVEDLA 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: Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv |
Molecular weight | Theoretical: 147.438344 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: VNFFDELRIG LATAEDIRQW SYGEVKKPET INYRTLKPEK DGLFCEKIFG PTRDWECYCG KYKRVRFKGI ICERCGVEVT RAKVRRERM GHIELAAPVT HIWYFKGVPS RLGYLLDLAP KDLEKIIYFA AYVITSVDEE MRHNELSTLE AEMAVERKAV E DQRDGELE ...String: VNFFDELRIG LATAEDIRQW SYGEVKKPET INYRTLKPEK DGLFCEKIFG PTRDWECYCG KYKRVRFKGI ICERCGVEVT RAKVRRERM GHIELAAPVT HIWYFKGVPS RLGYLLDLAP KDLEKIIYFA AYVITSVDEE MRHNELSTLE AEMAVERKAV E DQRDGELE ARAQKLEADL AELEAEGAKA DARRKVRDGG EREMRQIRDR AQRELDRLED IWSTFTKLAP KQLIVDENLY RE LVDRYGE YFTGAMGAES IQKLIENFDI DAEAESLRDV IRNGKGQKKL RALKRLKVVA AFQQSGNSPM GMVLDAVPVI PPE LRPMVQ LDGGRFATSD LNDLYRRVIN RNNRLKRLID LGAPEIIVNN EKRMLQESVD ALFDNGRRGR PVTGPGNRPL KSLS DLLKG KQGRFRQNLL GKRVDYSGRS VIVVGPQLKL HQCGLPKLMA LELFKPFVMK RLVDLNHAQN IKSAKRMVER QRPQV WDVL EEVIAEHPVL LNRAPTLHRL GIQAFEPMLV EGKAIQLHPL VCEAFNADFD GDQMAVHLPL SAEAQAEARI LMLSSN NIL SPASGRPLAM PRLDMVTGLY YLTTEVPGDT GEYQPASGDH PETGVYSSPA EAIMAADRGV LSVRAKIKVR LTQLRPP VE IEAELFGHSG WQPGDAWMAE TTLGRVMFNE LLPLGYPFVN KQMHKKVQAA IINDLAERYP MIVVAQTVDK LKDAGFYW A TRSGVTVSMA DVLVPPRKKE ILDHYEERAD KVEKQFQRGA LNHDERNEAL VEIWKEATDE VGQALREHYP DDNPIITIV DSGATGNFTQ TRTLAGMKGL VTNPKGEFIP RPVKSSFREG LTVLEYFINT HGARKGLADT ALRTADSGYL TRRLVDVSQD VIVREHDCQ TERGIVVELA ERAPDGTLIR DPYIETSAYA RTLGTDAVDE AGNVIVERGQ DLGDPEIDAL LAAGITQVKV R SVLTCATS TGVCATCYGR SMATGKLVDI GEAVGIVAAQ SIGEPGTQLT MRTFHQGGVG EDITGGLPRV QELFEARVPR GK APIADVT GRVRLEDGER FYKITIVPDD GGEEVVYDKI SKRQRLRVFK HEDGSERVLS DGDHVEVGQQ LMEGSADPHE VLR VQGPRE VQIHLVREVQ EVYRAQGVSI HDKHIEVIVR QMLRRVTIID SGSTEFLPGS LIDRAEFEAE NRRVVAEGGE PAAG RPVLM GITKASLATD SWLSAASFQE TTRVLTDAAI NCRSDKLNGL KENVIIGKLI PAGTGINRYR NIAVQPTEEA RAAAY TIPS YEDQYYSPDF GAATGAAVPL DDYGYSDYRH HHHHH 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: Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv |
Molecular weight | Theoretical: 11.85114 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSISQSDASL AAVPAVDQFD PSSGASGGYD TPLGITNPPI DELLDRVSSK YALVIYAAKR ARQINDYYNQ LGEGILEYVG PLVEPGLQE KPLSIALREI HADLLEHTEG E UniProtKB: DNA-directed RNA polymerase subunit omega |
-Macromolecule #5: RNA polymerase sigma factor SigB
Macromolecule | Name: RNA polymerase sigma factor SigB / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv |
Molecular weight | Theoretical: 38.572773 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MADAPTRATT SRVDSDLDAQ SPAADLVRVY LNGIGKTALL NAAGEVELAK RIEAGLYAEH LLETRKRLG ENRKRDLAAV VRDGEAARRH LLEANLRLVV SLAKRYTGRG MPLLDLIQEG NLGLIRAMEK FDYTKGFKFS T YATWWIRQ ...String: MGSSHHHHHH SSGLVPRGSH MADAPTRATT SRVDSDLDAQ SPAADLVRVY LNGIGKTALL NAAGEVELAK RIEAGLYAEH LLETRKRLG ENRKRDLAAV VRDGEAARRH LLEANLRLVV SLAKRYTGRG MPLLDLIQEG NLGLIRAMEK FDYTKGFKFS T YATWWIRQ AITRGMADQS RTIRLPVHLV EQVNKLARIK REMHQHLGRE ATDEELAAES GIPIDKINDL LEHSRDPVSL DM PVGSEEE APLGDFIEDA EAMSAENAVI AELLHTDIRS VLATLDEREH QVIRLRFGLD DGQPRTLDQI GKLFGLSRER VRQ IERDVM SKLRHGERAD RLRSYAS UniProtKB: RNA polymerase sigma factor SigB |
-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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.21 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/2 / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 7.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 3064 / Average exposure time: 8.0 sec. / Average electron dose: 49.6 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-7zf2: |