28YN | pdb_000028yn

VgrG1 from Pseudomonas aeruginosa (PA0091)

PDB DOI: https://doi.org/10.2210/pdb28YN/pdb
EM Map EMD-56974: EMDB EMDataResource

Classification: TOXIN
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-03-02 Released: 2026-06-10
Deposition Author(s): Zimmermann, M., Braun, T.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.63 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Affinity-tag-based microfluidic protein isolation enables high-resolution Cryo-EM from minimal starting material

Zimmermann, M., Braun, T.

(2026) bioRxiv

DOI: https://doi.org/10.64898/2026.05.20.726462

Macromolecule Content

Total Structure Weight: 223.91 kDa
Atom Count: 15,234
Modeled Residue Count: 1,926
Deposited Residue Count: 2,001
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type VI secretion system spike protein VgrG1a	A, B, C	667	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: vgrG1a, PA0091
UniProt
Find proteins for Q9I741 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I741 Go to UniProtKB: Q9I741
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I741
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.63 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.7.1
MODEL REFINEMENT	PHENIX	2.0
MODEL REFINEMENT	Coot	1.1.15

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History (Full details and data files)

Version 1.0: 2026-06-10
Type: Initial release

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.