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Yorodumi- EMDB-12715: IMC-Arches C6 at 8.33A - Refinement with C6 symmetry of the Inner... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12715 | |||||||||||||||
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Title | IMC-Arches C6 at 8.33A - Refinement with C6 symmetry of the Inner Membrane Complex (IMC) with the Arches from the fully-assembled R388 type IV secretion system. | |||||||||||||||
Map data | Inner Membrane Complex (IMC) with the Arches, 6-fold symmetry and sharpened map | |||||||||||||||
Sample |
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Keywords | type IV secretion system / type 4 secretion system / T4SS / IMC / inner membrane complex / inner membrane / arches / periplasmic / R388 plasmid / conjugation / bacterial secretion / secretion / secretion system / protein complex / VirB3 / VirB4 / VirB8 / TrwM / TrwK / TrwG / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Function and homology information protein secretion by the type IV secretion system / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.6 Å | |||||||||||||||
Authors | Mace K / Vadakkepat AK | |||||||||||||||
Funding support | United Kingdom, 4 items
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Citation | Journal: Nature / Year: 2022 Title: Cryo-EM structure of a type IV secretion system. Authors: Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong ...Authors: Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong / Gabriel Waksman / Abstract: Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance ...Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance genes spread among bacterial populations. In Gram-negative bacteria, conjugation is mediated by a large transport apparatus-the conjugative type IV secretion system (T4SS)-produced by the donor cell and embedded in both its outer and inner membranes. The T4SS also elaborates a long extracellular filament-the conjugative pilus-that is essential for DNA transfer. Here we present a high-resolution cryo-electron microscopy (cryo-EM) structure of a 2.8 megadalton T4SS complex composed of 92 polypeptides representing 8 of the 10 essential T4SS components involved in pilus biogenesis. We added the two remaining components to the structural model using co-evolution analysis of protein interfaces, to enable the reconstitution of the entire system including the pilus. This structure describes the exceptionally large protein-protein interaction network required to assemble the many components that constitute a T4SS and provides insights on the unique mechanism by which they elaborate pili. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_12715.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-12715-v30.xml emd-12715.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
Images | emd_12715.png | 61.6 KB | ||
Masks | emd_12715_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-12715.cif.gz | 6.2 KB | ||
Others | emd_12715_additional_1.map.gz emd_12715_half_map_1.map.gz emd_12715_half_map_2.map.gz | 31.1 MB 59.3 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12715 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12715 | HTTPS FTP |
-Validation report
Summary document | emd_12715_validation.pdf.gz | 1009.3 KB | Display | EMDB validaton report |
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Full document | emd_12715_full_validation.pdf.gz | 1008.9 KB | Display | |
Data in XML | emd_12715_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | emd_12715_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12715 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12715 | HTTPS FTP |
-Related structure data
Related structure data | 7o41MC 7o3jC 7o3tC 7o3vC 7o42C 7o43C 7oiuC 7q1vC M: atomic model generated by this map C: citing same article (ref.) |
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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_12715.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Inner Membrane Complex (IMC) with the Arches, 6-fold symmetry and sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.134 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_12715_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Inner Membrane Complex (IMC) with the Arches, 6-fold...
File | emd_12715_additional_1.map | ||||||||||||
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Annotation | Inner Membrane Complex (IMC) with the Arches, 6-fold symmetry and unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Inner Membrane Complex (IMC) with the Arches, 6-fold...
File | emd_12715_half_map_1.map | ||||||||||||
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Annotation | Inner Membrane Complex (IMC) with the Arches, 6-fold symmetry - Half_B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Inner Membrane Complex (IMC) with the Arches, 6-fold...
File | emd_12715_half_map_2.map | ||||||||||||
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Annotation | Inner Membrane Complex (IMC) with the Arches, 6-fold symmetry - Half_A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Type IV secretion system complex
Entire | Name: Type IV secretion system complex |
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Components |
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-Supramolecule #1: Type IV secretion system complex
Supramolecule | Name: Type IV secretion system complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: R388 plasmid |
Molecular weight | Theoretical: 2.808 MDa |
-Macromolecule #1: TrwM protein
Macromolecule | Name: TrwM protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 12.292585 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKPPQQQHEA FPLFKGATRL PTIWGVPMIP LMAMVMGVAV IALTVSIWWW ALVPPLWFIM AQITKNDDKA FRIWWLWIDT KFRNRNKGF WGASSYSPAN YRKRR UniProtKB: TrwM protein |
-Macromolecule #2: TrwK protein
Macromolecule | Name: TrwK protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 93.76993 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGAIESRKLL ASETPVGQFI PYSHHVTDTI ISTKNAEYLS VWKIDGRSHQ SASEADVFQW IRELNNTLRG ISSANLSLWT HIVRRRVYE YPDAEFDNVF CRQLDEKYRE SFTGYNLMVN DLYLTVVYRP VSDKVLSFFA KRERETPDQK KHRQESCIKA L EDINRTLG ...String: MGAIESRKLL ASETPVGQFI PYSHHVTDTI ISTKNAEYLS VWKIDGRSHQ SASEADVFQW IRELNNTLRG ISSANLSLWT HIVRRRVYE YPDAEFDNVF CRQLDEKYRE SFTGYNLMVN DLYLTVVYRP VSDKVLSFFA KRERETPDQK KHRQESCIKA L EDINRTLG QSFKRYGAEL LSVYEKGGHA FSAPLEFLAR LVNGEHIPMP ICRDRFSDYM AVNRPMFSKW GEVGELRSLT GL RRFGMLE IREYDDATEP GQLNVLLESD YEFVLTHSFS VLSRPAAKEY LQRHQKNLID ARDVATDQIE EIDEALNQLI SGH FVMGEH HCTLTVYGET VQQVRDNLAH ASAAMLDVAV LPKPVDLALE AGYWAQLPAN WQWRPRPAPI TSLNFLSFSP FHNF MSGKP TGNPWGPAVT ILKTVSGTPL YFNFHASKEE EDATDKRLLG NTMLIGQSSS GKTVLLGFLL AQAQKFKPTI VAFDK DRGM EISIRAMGGR YLPLKTGEPS GFNPFQLPPT HANLIFLKQF VKKLAAAGGE VTHRDEEEID QAITAMMSDS IDKSLR RLS LLLQFLPNPR SDDMDARPTV HARLVKWCEG GDYGWLFDNP TDALDLSTHQ IYGFDITEFL DNPEARTPVM MYLLYRT ES MIDGRRFMYV FDEFWKPLQD EYFEDLAKNK QKTIRKQNGI FVFATQEPSD ALESNIAKTL IQQCATYIFL ANPKADYE D YTQGFKLTDS EFELVRGLGE FSRRFLIKQG DQSALAEMNL GKFRTIVDGE TVERDFDDEL LVLSGTPDNA EIAESIIAE VGDDPAVWLP IFLDRVKAER SDV UniProtKB: Type IV secretion system protein virB4 |
-Macromolecule #3: TrwG protein
Macromolecule | Name: TrwG protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 25.799994 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSKKQPKPVK AEQLKSYYEE SRGLERDLIG EFVKSRKTAW RVATASGLFG LLGMVCGIVG FSQPAPAPLV LRVDNATGAV DVVTTLREH ESSYGEVVDT YWLNQYVLNR EAYDYNTIQM NYDTTALLSA PAVQQDYYKL FDGSNARDRV LGNKARITVR V RSIQPNGR ...String: MSKKQPKPVK AEQLKSYYEE SRGLERDLIG EFVKSRKTAW RVATASGLFG LLGMVCGIVG FSQPAPAPLV LRVDNATGAV DVVTTLREH ESSYGEVVDT YWLNQYVLNR EAYDYNTIQM NYDTTALLSA PAVQQDYYKL FDGSNARDRV LGNKARITVR V RSIQPNGR GQATVRFTTQ QHNSNGTVEA PQHQIATIGY TYIGAPMRSS DRLLNPLGFQ VTSYRADPEI LNN UniProtKB: TrwG protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: CryoSPARC ab-initio |
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Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126975 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: OTHER / Details: Stochastic gradient descent (SGD) |