9PHF | pdb_00009phf

Vpb4Aa2 pore complex in C7 symmetry

PDB DOI: https://doi.org/10.2210/pdb9PHF/pdb
EM Map EMD-71647: EMDB EMDataResource

Classification: TOXIN
Organism(s): Bacillus thuringiensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-07-09 Released: 2026-06-24
Deposition Author(s): Wirawan, R., Spicer, B.A., Lupton, C.J., Venugopal, H., Berry, C., Dunstone, M.A.
Funding Organization(s): Other private, Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.20 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

Structural basis for independent pore function of Vpb4 from Bacillus thuringiensis

Wirawan, R., Jamieson, W.D., Baird, H.M., Berry, C., Lupton, C.J., Venugopal, H., Valentin-Alvarado, L.E., Best, H.L., Jones, D.D., Wiliamson, L.J., Al-Maslookhi, H.S., Castell, O.K., Dunstone, M.A., Spicer, B.A.

(2026) Nat Commun

DOI: https://doi.org/10.1038/s41467-026-74567-y

Macromolecule Content

Total Structure Weight: 588.48 kDa
Atom Count: 35,021
Modeled Residue Count: 4,438
Deposited Residue Count: 5,250
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vip4	A, B, C, D, E A, B, C, D, E, F, G	750	Bacillus thuringiensis	Mutation(s): 0 Gene Names: vip4
UniProt
Find proteins for V9I0N3 (Bacillus thuringiensis) Explore V9I0N3 Go to UniProtKB: V9I0N3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	V9I0N3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain X [auth F] SDF format, chain Z [auth G] SDF format, chain Y [auth F] SDF format, chain V [auth E] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth B] SDF format, chain J [auth A] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] MOL2 format, chain Z [auth G] MOL2 format, chain Y [auth F] MOL2 format, chain V [auth E] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain X [auth F] mmCIF format, chain Z [auth G] mmCIF format, chain Y [auth F] mmCIF format, chain V [auth E] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A]	AA [auth G] BA [auth G] H [auth A] I [auth A] J [auth A] AA [auth G], BA [auth G], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth C], O [auth C], P [auth C], Q [auth D], R [auth D], S [auth D], T [auth E], U [auth E], V [auth E], W [auth F], X [auth F], Y [auth F], Z [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth G]

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	RELION	5.0

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		Georgina Sweet Award for Women in Quantitative Biomedical Science
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T019948/1, BB/S002774/1, BB/M009122/1