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- PDB-9vgf: Cryo-EM structure of CagX-CagY complex with C17 symmetry -

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Basic information

Entry
Database: PDB / ID: 9vgf
TitleCryo-EM structure of CagX-CagY complex with C17 symmetry
Components
  • Cag pathogenicity island protein X
  • Type IV secretion system apparatus protein CagY
KeywordsSTRUCTURAL PROTEIN / Type IV secretion system / Helicobacter pylori / Periplasmic ring complex
Function / homologyType IV secretion system CagX conjugation protein / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / Cag pathogenicity island protein X
Function and homology information
Biological speciesHelicobacter pylori G27 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsMok, C.Y. / Chu, H.Y. / Au, S.W.N.
Funding support Hong Kong, 2items
OrganizationGrant numberCountry
Other privateStrategic Partnership Award for Research Collaboration
The University Grants Committee, Research Grants Council (RGC)14121619 Hong Kong
CitationJournal: To Be Published
Title: Cryo-EM structure of CagX-CagY complex with C17 symmetry
Authors: Mok, C.Y. / Chu, H.Y. / Au, S.W.N.
History
DepositionJun 13, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AX: Cag pathogenicity island protein X
AY: Type IV secretion system apparatus protein CagY
BX: Cag pathogenicity island protein X
BY: Type IV secretion system apparatus protein CagY
CX: Cag pathogenicity island protein X
CY: Type IV secretion system apparatus protein CagY
DX: Cag pathogenicity island protein X
DY: Type IV secretion system apparatus protein CagY
EX: Cag pathogenicity island protein X
EY: Type IV secretion system apparatus protein CagY
FX: Cag pathogenicity island protein X
FY: Type IV secretion system apparatus protein CagY
GX: Cag pathogenicity island protein X
GY: Type IV secretion system apparatus protein CagY
HX: Cag pathogenicity island protein X
HY: Type IV secretion system apparatus protein CagY
IX: Cag pathogenicity island protein X
IY: Type IV secretion system apparatus protein CagY
JX: Cag pathogenicity island protein X
JY: Type IV secretion system apparatus protein CagY
KX: Cag pathogenicity island protein X
KY: Type IV secretion system apparatus protein CagY
LX: Cag pathogenicity island protein X
LY: Type IV secretion system apparatus protein CagY
MX: Cag pathogenicity island protein X
MY: Type IV secretion system apparatus protein CagY
NX: Cag pathogenicity island protein X
NY: Type IV secretion system apparatus protein CagY
OX: Cag pathogenicity island protein X
OY: Type IV secretion system apparatus protein CagY
PX: Cag pathogenicity island protein X
PY: Type IV secretion system apparatus protein CagY
QX: Cag pathogenicity island protein X
QY: Type IV secretion system apparatus protein CagY


Theoretical massNumber of molelcules
Total (without water)1,800,59634
Polymers1,800,59634
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Cag pathogenicity island protein X


Mass: 57815.992 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori G27 (bacteria) / Gene: cagX, HPG27_487 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5Z6Q0
#2: Protein
Type IV secretion system apparatus protein CagY


Mass: 48101.406 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
Details: Sequence has been deposited at Genbank with accession code CP001173.1
Source: (gene. exp.) Helicobacter pylori G27 (bacteria) / Gene: cagY / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationY

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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: CagX-CagY complex with C17 symmetry / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Helicobacter pylori G27 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 373053 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00332249
ELECTRON MICROSCOPYf_angle_d0.60543571
ELECTRON MICROSCOPYf_dihedral_angle_d4.8914216
ELECTRON MICROSCOPYf_chiral_restr0.0434913
ELECTRON MICROSCOPYf_plane_restr0.0045627

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