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- EMDB-12709: Stalk C1 at 3.71A - Local refinement without symmetry of the Stal... -
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Open data
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Basic information
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Title | Stalk C1 at 3.71A - Local refinement without symmetry of the Stalk complex from the fully-assembled R388 type IV secretion system. | |||||||||||||||
![]() | Stalk local refinement C1 sharpened map | |||||||||||||||
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![]() | type IV secretion system / type 4 secretion system / T4SS / stalk / stalk complex / inner membrane / R388 plasmid / conjugation / bacterial secretion / secretion / secretion system / protein complex / VirB5 / VirB6 / TrwJ / TrwI / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Type IV secretion system, VirB5 / Type IV secretion system, VirB5-domain / Type IV secretion system proteins / Plasmid conjugal transfer TrbL/VirB6 / TrbL/VirB6 plasmid conjugal transfer protein / protein secretion by the type IV secretion system / membrane / TrwJ protein / TrwI protein![]() | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
![]() | Mace K / Vadakkepat AK | |||||||||||||||
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 | ![]() | 10.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.3 KB 18.3 KB | Display Display | ![]() |
Images | ![]() | 48.9 KB | ||
Masks | ![]() | 10.9 MB | ![]() | |
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() ![]() | 9.9 MB 10.1 MB 10.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 749.5 KB | Display | ![]() |
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Full document | ![]() | 749.1 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 8.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o3vMC ![]() 7o3jC ![]() 7o3tC ![]() 7o41C ![]() 7o42C ![]() 7o43C ![]() 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 | Stalk local refinement C1 sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.067 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Stalk local refinement C1 unsharpened map
File | emd_12709_additional_1.map | ||||||||||||
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Annotation | Stalk local refinement C1 unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Stalk local refinement C1 - Half-B
File | emd_12709_half_map_1.map | ||||||||||||
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Annotation | Stalk local refinement C1 - Half-B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Stalk local refinement C1 - Half-A
File | emd_12709_half_map_2.map | ||||||||||||
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Annotation | Stalk local refinement C1 - Half-A | ||||||||||||
Projections & Slices |
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Density Histograms |
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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: ![]() ![]() |
Molecular weight | Theoretical: 2.808 MDa |
-Macromolecule #1: TrwJ protein
Macromolecule | Name: TrwJ protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25.190461 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKKLVMTAAV AAILGAASPV MAQGIPVFDG TRALDFVQQF ARMKEQLDTA KDQLAEAQRM YEAVTGGRGL GDLMRNAQLR EYLPDDLRT VYDSANGGGY SGISGSINDI LRDERLNGSV ADMRRSIEER SRTAAATDKA VGLRAYEGAQ QRLAQIEGLM D EISRTQDQ ...String: MKKLVMTAAV AAILGAASPV MAQGIPVFDG TRALDFVQQF ARMKEQLDTA KDQLAEAQRM YEAVTGGRGL GDLMRNAQLR EYLPDDLRT VYDSANGGGY SGISGSINDI LRDERLNGSV ADMRRSIEER SRTAAATDKA VGLRAYEGAQ QRLAQIEGLM D EISRTQDQ KAIEELQARI AGEQAAIQNE TTKLQMIAQL RQAEQALISE QRRERNMRIL SSGNQGMPTI Q UniProtKB: TrwJ protein |
-Macromolecule #2: TrwI protein
Macromolecule | Name: TrwI protein / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 35.324172 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAFELFTPLF NKIDQTTATY VTDISSRAIA AITPVVSVGL TLGFITYGWL IIRGAVEMPV AEFLNRCLRI GIIVSIALAG GLYQGEIAN AITTVPDELA SALLGNPTQG ASAAALVDQS AQQGFDRASE AFEEAGFFSS DGLLYGLFGI IILLATGLLA A IGGAFLLL ...String: MAFELFTPLF NKIDQTTATY VTDISSRAIA AITPVVSVGL TLGFITYGWL IIRGAVEMPV AEFLNRCLRI GIIVSIALAG GLYQGEIAN AITTVPDELA SALLGNPTQG ASAAALVDQS AQQGFDRASE AFEEAGFFSS DGLLYGLFGI IILLATGLLA A IGGAFLLL AKIALALLAG LGPLFILALI WQPTHRFFDQ WAQQVLNYGL LIVLFAAVFG LLMQIFGSYM ADLRFDGAQN VA YAIGGSV ILSIVSIVLL MQLPSIASGL AGGIGLGYMW ELRSMRSGAG AAMRGGRAMA RGARAAPGAA RGAAVGAANM AKT VATGGA GVARAAAGYF RGRKAG UniProtKB: TrwI protein |
-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: 7.6 |
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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 K3 (6k x 4k) / Average electron dose: 57.5 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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 566815 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: OTHER / Details: Stochastic gradient descent (SGD) |