9V2S | pdb_00009v2s

Cryo-EM structure of Runella bGSDM pore

PDB DOI: https://doi.org/10.2210/pdb9V2S/pdb
EM Map EMD-64739: EMDB EMDataResource

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Runella zeae DSM 19591
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-20 Released: 2026-07-08
Deposition Author(s): Su, Z., Feng, Y., Gan, J.H., Feng, Y.J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.25 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of Runella bGSDM pore

Feng, Y.J., Gan, J.H., Feng, Y., Su, Z.

To be published.

Macromolecule Content

Total Structure Weight: 2,528.19 kDa
Atom Count: 162,012
Modeled Residue Count: 20,148
Deposited Residue Count: 22,264
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gasdermin bGSDM, N-terminus	A AA [auth a] AB [auth 1] AC [auth AQ] B A, AA [auth a], AB [auth 1], AC [auth AQ], B, BA [auth b], BB [auth 2], BC [auth AR], C, CA [auth c], CB [auth 3], CC [auth AS], D, DA [auth d], DB [auth 4], DC [auth AT], E, EA [auth e], EB [auth 5], EC [auth AU], F, FA [auth f], FB [auth 6], FC [auth AV], G, GA [auth g], GB [auth 7], GC [auth AW], H, HA [auth h], HB [auth 8], HC [auth AX], I, IA [auth i], IB [auth 9], IC [auth AY], J, JA [auth j], JB [auth 0], JC [auth AZ], K, KA [auth k], KB [auth AA], KC [auth Aa], L, LA [auth l], LB [auth AB], LC [auth Ab], M, MA [auth m], MB [auth AC], MC [auth Ac], N, NA [auth n], NB [auth AD], NC [auth Ad], O, OA [auth o], OB [auth AE], P, PA [auth p], PB [auth AF], Q, QA [auth q], QB [auth AG], R, RA [auth r], RB [auth AH], S, SA [auth s], SB [auth AI], T, TA [auth t], TB [auth AJ], U, UA [auth u], UB [auth AK], V, VA [auth v], VB [auth AL], W, WA [auth w], WB [auth AM], X, XA [auth x], XB [auth AN], Y, YA [auth y], YB [auth AO], Z, ZA [auth z], ZB [auth AP]	242	Runella zeae DSM 19591	Mutation(s): 0 Gene Names: G563DRAFT_02010
UniProt
Find proteins for P0DV48 (Runella zeae (strain ATCC BAA-293 / DSM 19591 / LMG 21438 / NS12)) Explore P0DV48 Go to UniProtKB: P0DV48
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DV48
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.25 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2026-07-08
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.