9VP2 | pdb_00009vp2

CryoEM structure of cyclised H-pilus (D69A)

PDB DOI: https://doi.org/10.2210/pdb9VP2/pdb
EM Map EMD-65234: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Salmonella enterica subsp. enterica serovar Typhi
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-07-02 Released: 2025-12-24
Deposition Author(s): Ishimoto, N., Beis, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.15 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

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

Literature

Surface electrostatic potential affects mating pilus functionality

He, S., Ishimoto, N., Wong, J., David, S., Beis, K., Frankel, G.

To be published.

Macromolecule Content

Total Structure Weight: 8.28 kDa
Atom Count: 544
Modeled Residue Count: 69
Deposited Residue Count: 74
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pilin	A	74	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 1 Gene Names: trhA, HCM1.67
UniProt
Find proteins for Q935P5 (Salmonella typhi) Explore Q935P5 Go to UniProtKB: Q935P5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q935P5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LHG (Subject of Investigation/LOI) Query on LHG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.15 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-12-24
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 R01GM157729.