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- PDB-6odi: Structure of CagY from a cryo-EM reconstruction of a T4SS -

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Basic information

Entry
Database: PDB / ID: 6odi
TitleStructure of CagY from a cryo-EM reconstruction of a T4SS
ComponentsType IV secretion system apparatus protein CagY
KeywordsTRANSLOCASE / T4SS / Secretion / H. pylori
Function / homology
Function and homology information


membrane => GO:0016020 / membrane
Similarity search - Function
CagY type 1 repeat / CagY type 1 repeat / DC-EC / DC-EC Repeat / Type IV secretion system, VirB10/TrbI / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI
Similarity search - Domain/homology
Type IV secretion system apparatus protein CagY / Cag pathogenicity island protein (Cag7)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChung, J.M. / Sheedlo, M.J. / Campbell, A. / Sawhney, N. / Frick-Cheng, A.E. / Lacy, D.B. / Cover, T.L. / Ohi, M.D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH AI118932 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA116087 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other government1I01BX004447 United States
CitationJournal: Elife / Year: 2019
Title: Structure of the Cag type IV secretion system.
Authors: Jeong Min Chung / Michael J Sheedlo / Anne M Campbell / Neha Sawhney / Arwen E Frick-Cheng / Dana Borden Lacy / Timothy L Cover / Melanie D Ohi /
Abstract: Bacterial type IV secretion systems (T4SSs) are molecular machines that can mediate interbacterial DNA transfer through conjugation and delivery of effector molecules into host cells. The Cag T4SS ...Bacterial type IV secretion systems (T4SSs) are molecular machines that can mediate interbacterial DNA transfer through conjugation and delivery of effector molecules into host cells. The Cag T4SS translocates CagA, a bacterial oncoprotein, into gastric cells, contributing to gastric cancer pathogenesis. We report the structure of a membrane-spanning Cag T4SS assembly, which we describe as three sub-assemblies: a 14-fold symmetric outer membrane core complex (OMCC), 17-fold symmetric periplasmic ring complex (PRC), and central stalk. Features that differ markedly from those of prototypical T4SSs include an expanded OMCC and unexpected symmetry mismatch between the OMCC and PRC. This structure is one of the largest bacterial secretion system assemblies ever reported and illustrates the remarkable structural diversity that exists among bacterial T4SSs.
History
DepositionMar 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 7, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
b: Type IV secretion system apparatus protein CagY
c: Type IV secretion system apparatus protein CagY
d: Type IV secretion system apparatus protein CagY
e: Type IV secretion system apparatus protein CagY
f: Type IV secretion system apparatus protein CagY
g: Type IV secretion system apparatus protein CagY
h: Type IV secretion system apparatus protein CagY
i: Type IV secretion system apparatus protein CagY
j: Type IV secretion system apparatus protein CagY
k: Type IV secretion system apparatus protein CagY
l: Type IV secretion system apparatus protein CagY
m: Type IV secretion system apparatus protein CagY
n: Type IV secretion system apparatus protein CagY
o: Type IV secretion system apparatus protein CagY


Theoretical massNumber of molelcules
Total (without water)3,077,09714
Polymers3,077,09714
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Type IV secretion system apparatus protein CagY


Mass: 219792.656 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Helicobacter pylori (bacteria) / References: UniProt: A0A2J9KJK8, UniProt: O25262*PLUS

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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: Type IV secretion system apparatus protein CagY / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Helicobacter pylori (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in.
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 59.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameCategory
1RELIONparticle selection
4GctfCTF correction
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 24662
SymmetryPoint symmetry: C14 (14 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17159 / Symmetry type: POINT
Atomic model buildingB value: 68.95 / Protocol: AB INITIO MODEL / Space: REAL

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