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- EMDB-65209: Bacteroides fragilis NCTC9343 T6SS Hcp2-Hcp3 heterohexamer complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65209
TitleBacteroides fragilis NCTC9343 T6SS Hcp2-Hcp3 heterohexamer complex
Map data
Sample
  • Complex: Bacteroides fragilis NCTC9343 T6SS Hcp2-hcp3 heterohexamer complex
    • Protein or peptide: Bacteroides fragilis NCTC9343 T6SS Hcp2
    • Protein or peptide: Bacteroides fragilis NCTC9343 T6SS Hcp3
KeywordsBacteroides fragilis / T6SS / Hcp / STRUCTURAL PROTEIN
Function / homologyHemolysin coregulated protein (Hcp) TssD / Hemolysin coregulated protein Hcp (TssD) / type VI protein secretion system complex / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsZheng SN / Chen Z / Li WX / Gao X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)323B2003 China
CitationJournal: Nat Commun / Year: 2026
Title: Conformational selection enables effector-specific delivery by Hcp heterohexamers in gut symbionts
Authors: Zheng SN / Li WX / Gao X
History
DepositionJun 30, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65209.png

Downloads & links

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Map

FileDownload / File: emd_65209.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 180 pix.
= 189.36 Å		1.05 Å/pix.
x 180 pix.
= 189.36 Å		1.05 Å/pix.
x 180 pix.
= 189.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.168
Minimum - Maximum-1.5131326 - 2.0835352
Average (Standard dev.)0.001573406 (±0.05248808)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 189.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65209_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65209_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacteroides fragilis NCTC9343 T6SS Hcp2-hcp3 heterohexamer complex

EntireName: Bacteroides fragilis NCTC9343 T6SS Hcp2-hcp3 heterohexamer complex
Components
  • Complex: Bacteroides fragilis NCTC9343 T6SS Hcp2-hcp3 heterohexamer complex
    • Protein or peptide: Bacteroides fragilis NCTC9343 T6SS Hcp2
    • Protein or peptide: Bacteroides fragilis NCTC9343 T6SS Hcp3

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Supramolecule #1: Bacteroides fragilis NCTC9343 T6SS Hcp2-hcp3 heterohexamer complex

SupramoleculeName: Bacteroides fragilis NCTC9343 T6SS Hcp2-hcp3 heterohexamer complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacteroides fragilis NCTC 9343 (bacteria)

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Macromolecule #1: Bacteroides fragilis NCTC9343 T6SS Hcp2

MacromoleculeName: Bacteroides fragilis NCTC9343 T6SS Hcp2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis NCTC 9343 (bacteria)
Molecular weightTheoretical: 16.112126 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MFGHKSFLRI GALGDSSISG LYKDSYELEN CHFSFNQGTN TDGKPQTDVR GGTLYLTYAG LPQDDMLRWI LNSKKYEDGA IVICDDSDE PLEKILFEQA ACTGLNIEYT QKGKAYIHTK IILQVRKIKV GETTFENRWT INE

UniProtKB: Uncharacterized protein

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Macromolecule #2: Bacteroides fragilis NCTC9343 T6SS Hcp3

MacromoleculeName: Bacteroides fragilis NCTC9343 T6SS Hcp3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis NCTC 9343 (bacteria)
Molecular weightTheoretical: 15.389363 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MELFSFLQVD SDLTAWFILD GQEYEMSHFD INFAQSVDHK GQPQDEVRGG IMSITLSQTL PENIYRWGMT SIPKNGSVIF KSKTTNPPL KINFINAYCI RFNRSIANEG GLESQLVISP DEMLINGISF DNHWVK

UniProtKB: Uncharacterized protein

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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

Concentration0.35 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 501091
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9vne:
Bacteroides fragilis NCTC9343 T6SS Hcp2-Hcp3 heterohexamer complex

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