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- PDB-8rt9: Stalk complex full-length structure (TrwJ/VirB5-TrwI/VirB6) from ... -

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Basic information

Entry
Database: PDB / ID: 8rt9
TitleStalk complex full-length structure (TrwJ/VirB5-TrwI/VirB6) from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Components
  • TrwI protein
  • TrwJ protein
KeywordsMEMBRANE PROTEIN / type IV secretion system type 4 secretion system T4SS Stalk R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB5 VirB6 TrwI TrwJ
Function / homologyType 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
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsMace, K. / Waksman, G.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust098302 United Kingdom
Wellcome Trust217089 United Kingdom
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: To Be Published / Year: 2024
Title: Cryo-EM structure of a conjugative type 4 secretion system identifies a molecular switch regulating conjugative pilus biogenesis
Authors: Mace, K. / Waksman, G.
History
DepositionJan 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TrwJ protein
B: TrwJ protein
C: TrwJ protein
D: TrwJ protein
E: TrwJ protein
F: TrwI protein
G: TrwI protein
H: TrwI protein
I: TrwI protein
J: TrwI protein


Theoretical massNumber of molelcules
Total (without water)302,57310
Polymers302,57310
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
TrwJ protein


Mass: 25190.461 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwJ / Production host: Escherichia coli (E. coli) / References: UniProt: O50331
#2: Protein
TrwI protein


Mass: 35324.172 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwI / Production host: Escherichia coli (E. coli) / References: UniProt: O50333

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Stalk complex from the fully-assembled R388 type IV secretion system
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 3300 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 57.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.18.2_3874:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104720 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00718681
ELECTRON MICROSCOPYf_angle_d0.76725292
ELECTRON MICROSCOPYf_dihedral_angle_d21.4856675
ELECTRON MICROSCOPYf_chiral_restr0.0522984
ELECTRON MICROSCOPYf_plane_restr0.0043282

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