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- EMDB-12717: Dimer TrwK/VirB4unbound C1 at 3.49A - Local refinement without sy... -
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Open data
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Basic information
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Title | Dimer TrwK/VirB4unbound C1 at 3.49A - Local refinement without symmetry of the TrwK/VirB4unbound dimer complex from the R388 type IV secretion system. | |||||||||||||||
![]() | Local refinement TrwK/VirB4unbound dimer complex without symmetry sharpened map | |||||||||||||||
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![]() | type IV secretion system / type 4 secretion system / T4SS / inner membrane complex / inner membrane / R388 plasmid / conjugation / ATPase / bacterial secretion / secretion / secretion system / protein complex / VirB4 / TrwK / dimer / Hcp / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | ![]() | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||
![]() | Vadakkepat AK / Mace K | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.3 KB 17.3 KB | Display Display | ![]() |
Images | ![]() | 84.2 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() ![]() | 6.9 MB 95.6 MB 95.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o43MC ![]() 7o3jC ![]() 7o3tC ![]() 7o3vC ![]() 7o41C ![]() 7o42C ![]() 7oiuC ![]() 7q1vC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Local refinement TrwK/VirB4unbound dimer complex without symmetry sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.048 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Local refinement TrwK/VirB4unbound dimer complex without symmetry unsharpened...
File | emd_12717_additional_1.map | ||||||||||||
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Annotation | Local refinement TrwK/VirB4unbound dimer complex without symmetry unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Local refinement TrwK/VirB4unbound dimer complex - Half-A
File | emd_12717_half_map_1.map | ||||||||||||
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Annotation | Local refinement TrwK/VirB4unbound dimer complex - Half-A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Local refinement TrwK/VirB4unbound dimer complex - Half-B
File | emd_12717_half_map_2.map | ||||||||||||
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Annotation | Local refinement TrwK/VirB4unbound dimer complex - Half-B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Hexamer complex of Apo-TrwK/VirB4 with Hcp1
Entire | Name: Hexamer complex of Apo-TrwK/VirB4 with Hcp1 |
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Components |
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-Supramolecule #1: Hexamer complex of Apo-TrwK/VirB4 with Hcp1
Supramolecule | Name: Hexamer complex of Apo-TrwK/VirB4 with Hcp1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: TrwK protein
Macromolecule | Name: TrwK protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 94.202328 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 SDVGSGSGS UniProtKB: Type IV secretion system protein virB4 |
-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: 8 |
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Vitrification | Cryogen name: ETHANE |
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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) / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER / Details: CryoSPARC ab-initio |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 214048 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: OTHER / Details: Stochastic gradient descent (SGD) |