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- EMDB-65051: Cryo-EM structure of CagX-CagY complex with C16 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-65051
TitleCryo-EM structure of CagX-CagY complex with C16 symmetry
Map data
Sample
  • Complex: CagX-CagY complex with C16 symmetry
    • Protein or peptide: Cag pathogenicity island protein X
    • Protein or peptide: Type IV secretion system apparatus protein CagY
KeywordsType IV secretion system / Helicobacter pylori / Periplasmic ring complex / STRUCTURAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsMok CY / Chu HY / Au SWN
Funding support Hong Kong, 2 items
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 C16 symmetry
Authors: Mok CY / Chu HY / Au SWN
History
DepositionJun 15, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65051.png

Downloads & links

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Map

FileDownload / File: emd_65051.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 352 pix.
= 292.16 Å		0.83 Å/pix.
x 352 pix.
= 292.16 Å		0.83 Å/pix.
x 352 pix.
= 292.16 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.171
Minimum - Maximum-1.066665 - 1.7641534
Average (Standard dev.)0.0023229078 (±0.053149294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 292.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65051_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65051_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CagX-CagY complex with C16 symmetry

EntireName: CagX-CagY complex with C16 symmetry
Components
  • Complex: CagX-CagY complex with C16 symmetry
    • Protein or peptide: Cag pathogenicity island protein X
    • Protein or peptide: Type IV secretion system apparatus protein CagY

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Supramolecule #1: CagX-CagY complex with C16 symmetry

SupramoleculeName: CagX-CagY complex with C16 symmetry / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Helicobacter pylori G27 (bacteria)

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Macromolecule #1: Cag pathogenicity island protein X

MacromoleculeName: Cag pathogenicity island protein X / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori G27 (bacteria)
Molecular weightTheoretical: 57.815992 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: APDIKNFNRG RVKVVNKKIA YLGDEKPITI WTSLDNVTVI QLEKDETISY ITTGFNKGWS IVPNSNHIFI QPKSVKSNLM FEKEAVNFA LMTRDYQEFL KTKKLIVDAP DPKELEEQKK ALEKEKEAKE QAQKVQKDKR EKRKEERAKN RANLENLTNA M SNPQNLSN ...String:
APDIKNFNRG RVKVVNKKIA YLGDEKPITI WTSLDNVTVI QLEKDETISY ITTGFNKGWS IVPNSNHIFI QPKSVKSNLM FEKEAVNFA LMTRDYQEFL KTKKLIVDAP DPKELEEQKK ALEKEKEAKE QAQKVQKDKR EKRKEERAKN RANLENLTNA M SNPQNLSN NKNLSELIKQ QRENELDQME RLEDMQEQAQ ANALKQIEEL NKKQAEETIK QRAKDKISIK TDKSQKSPED NS IELSPSD SAWRTNLVVR TNKALYQFIL RIAQKDNFAS AYLTVKLEYP QRHEVSSVIE EELKKREEAK RQRELIKQEN LNT TAYINR VMMASNEQII NKEKIREEKQ KIILDQAKAL ETQYVHNALK RNPVPRNYNY YQAPEKRSKH IMPSEIFDDG TFTY FGFKN ITLQPAIFVV QPDGKLSMTD AAIDPNMTNL GLRWYRVNEI AEKFKLIKDK ALVTVINKGY GKNPLTKNYN IKNYG ELER VIKKLPLVRD K

UniProtKB: Cag pathogenicity island protein X

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Macromolecule #2: Type IV secretion system apparatus protein CagY

MacromoleculeName: Type IV secretion system apparatus protein CagY / type: protein_or_peptide / ID: 2
Details: Sequence has been deposited at Genbank with accession code CP001173.1
Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori G27 (bacteria)
Molecular weightTheoretical: 48.101406 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: LSKTERLHQA SECLDNLDDP TDQEAIEQCL EGLSDSERAL ILGIKRQADE VDLIYSELRN RKTFDNMAAK GYPLLPMDFK NGGDIATIN ATNVDADKIA SDNPIYASIE PDIAKQYETE KTIKDKNLEA KLAKALGGNK KDDDKEKSKK STAEAKAENN K IDKDVAET ...String:
LSKTERLHQA SECLDNLDDP TDQEAIEQCL EGLSDSERAL ILGIKRQADE VDLIYSELRN RKTFDNMAAK GYPLLPMDFK NGGDIATIN ATNVDADKIA SDNPIYASIE PDIAKQYETE KTIKDKNLEA KLAKALGGNK KDDDKEKSKK STAEAKAENN K IDKDVAET AKNISEIALK NKKEKSGEFV DENGNPIDDK KKAEKQDETS PVKQAFIGKS DPTFVLAQYT PIEITLTSKV DA TLTGIVS GVVAKDVWNM NGTMILLDKG TKVYGNYQSV KGGTPIMTRL MIVFTKAITP DGVIIPLANA QAAGMLGEAG VDG YVNNHF MKRIGFAVIA SVVNSFLQTA PIIALDKLIG LGKGRSERTP EFNYALGQAI NGSMQSSAQM SNQILGQLMN IPPS FYKNE GDSIKILTMD DIDFSGVYDV KITNKSVVDE IIKQST

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6x6j

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 406996
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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