8ZSF | pdb_00008zsf

CryoEM Helical Structure of KomC

PDB DOI: https://doi.org/10.2210/pdb8ZSF/pdb
EM Map EMD-60413: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-06-05 Released: 2025-12-10
Deposition Author(s): Hao, F., Kai, S., Min, L.
Funding Organization(s): Ministry of Education (MoE, Singapore)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.24 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

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

Literature

CryoEM Helical Structure of KomC

Hao, F., Eddie, T., Bin, W., Min, L.

To be published.

Macromolecule Content

Total Structure Weight: 367.87 kDa
Atom Count: 25,992
Modeled Residue Count: 3,168
Deposited Residue Count: 3,168
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sir2 family NAD-dependent protein deacetylase	A [auth D] B [auth A] C D [auth B] E [auth K] A [auth D], B [auth A], C, D [auth B], E [auth K], F [auth E], G [auth I], H [auth G], I [auth L], J [auth F], K [auth J], L [auth H]	264	Escherichia coli	Mutation(s): 0 Gene Names: GRW56_02060, GRW57_01895 EC: 2.3.1.286
UniProt
Find proteins for P75960 (Escherichia coli (strain K12)) Explore P75960 Go to UniProtKB: P75960
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P75960
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.24 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education (MoE, Singapore)	Singapore	--

Revision History (Full details and data files)

Version 1.0: 2025-12-10
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.