8CQ2

Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, C16S, C20S, C870S, T1279C mutant

PDB DOI: https://doi.org/10.2210/pdb8CQ2/pdb
EM Map EMD-16793: EMDB EMDataResource

Classification: TOXIN
Organism(s): Photorhabdus luminescens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-03-03 Released: 2024-03-13
Deposition Author(s): Nganga, P.N., Roderer, D., Belyy, A., Prumbaum, D., Raunser, S.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Kinetics of the syringe-like injection mechanism of Tc toxins

Nganga, P.N., Folz, J., Kucher, S., Roderer, D., Xu, Y., Sitsel, O., Belyy, A., Prumbaum, D., Assafa, T.E., Kuehnemuth, R., Dong, M., Seidel, C., Bordignon, E., Raunser, S.

To be published.

Macromolecule Content

Total Structure Weight: 1,426.65 kDa
Atom Count: 84,390
Modelled Residue Count: 10,610
Deposited Residue Count: 12,675
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TcdA1	A, B, C, D, E	2,535	Photorhabdus luminescens	Mutation(s): 4 Gene Names: tcdA, tcdA1
UniProt
Find proteins for Q9RN43 (Photorhabdus luminescens) Explore Q9RN43 Go to UniProtKB: Q9RN43
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9RN43
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2024-03-13
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.