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 31OD | pdb_000031od

Yersinia entomophaga holotoxin in its inverted pore state

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

A trefoil knot mimic and multiple pore states define the mechanism of a split-shell Tc toxin

Ng'ang'a, P.N., Raunser, S., Bader, R., Sitsel, O.

(2026) Pnas 

Macromolecule Content 

  • Total Structure Weight: 2,357.29 kDa 
  • Atom Count: 154,987 
  • Modeled Residue Count: 19,567 
  • Deposited Residue Count: 20,977 
  • Unique protein chains: 6

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Toxin subunit YenA1
A, F, I, L, O
1,164Yersinia entomophagaMutation(s): 0 
UniProt
Find proteins for B6A877 (Yersinia entomophaga)
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Toxin subunit YenA2
B, G, J, M, P
1,365Yersinia entomophagaMutation(s): 0 
UniProt
Find proteins for B6A878 (Yersinia entomophaga)
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Reference Sequence
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Chitinase 2
C, H, K, N, Q
633Yersinia entomophagaMutation(s): 0 
EC: 3.2.1.14
UniProt
Find proteins for B6A879 (Yersinia entomophaga)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Toxin subunit YenB1,487Yersinia entomophagaMutation(s): 0 
UniProt
Find proteins for B6A880 (Yersinia entomophaga)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Toxin subunit YenC2970Yersinia entomophagaMutation(s): 0 
UniProt
Find proteins for B6A882 (Yersinia entomophaga)
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Reference Sequence
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|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Chitinase 1
R, S, T, U, V
542Yersinia entomophagaMutation(s): 0 
EC: 3.2.1.14
UniProt
Find proteins for B6A876 (Yersinia entomophaga)
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UniProt GroupB6A876
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2026-11-11
    Type: Initial release