31QH | pdb_000031qh

Photorhabdus luminescens TcdA1 inverted pore state

PDB DOI: https://doi.org/10.2210/pdb31QH/pdb
EM Map EMD-58628: EMDB EMDataResource

Classification: TOXIN
Organism(s): Photorhabdus luminescens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-06-17 Released: 2026-11-11
Deposition Author(s): Ng'ang'a, P.N., Raunser, S., Bader, R., Sitsel, O.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 31QH

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: 1,426.88 kDa
Atom Count: 90,990
Modeled Residue Count: 11,460
Deposited Residue Count: 12,675
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Virulence plasmid A protein	A [auth D], B [auth E], C, D [auth A], E [auth B]	2,535	Photorhabdus luminescens	Mutation(s): 0 Gene Names: SAMN02982990_03606
UniProt
Find proteins for A0A1G5RA58 (Photorhabdus luminescens) Explore A0A1G5RA58 Go to UniProtKB: A0A1G5RA58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1G5RA58
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History (Full details and data files)

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