8XBL | pdb_00008xbl

Cryo-EM structure of colibactin assembly line polyketide synthase ClbC (apo state)

PDB DOI: https://doi.org/10.2210/pdb8XBL/pdb
EM Map EMD-38222: EMDB EMDataResource

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-12-06 Released: 2025-05-21
Deposition Author(s): Kim, J., Kim, M., Kang, J.Y.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.06 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

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

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

Literature

Cryo-EM structures of human microbiome-derived polyketide synthases that assemble genotoxic colibactin

Kim, M., Kim, J., Olinares, P.D.B., Park, J., Chait, B.T., Kang, J.Y.

(2025) Structure 33: 1-16

DOI: https://doi.org/10.1016/j.str.2025.04.017

Macromolecule Content

Total Structure Weight: 198.61 kDa
Atom Count: 11,509
Modeled Residue Count: 1,497
Deposited Residue Count: 1,816
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Colibactin polyketide synthase ClbC	A, B	908	Escherichia coli	Mutation(s): 0 Gene Names: clbC, C1Q91_004440, EPS76_08170, EWK56_24790, FPI65_12395, H0O51_09120, HMW38_22955, IFB95_004349
UniProt
Find proteins for Q0P7J3 (Escherichia coli) Explore Q0P7J3 Go to UniProtKB: Q0P7J3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0P7J3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.06 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF- 2019M3E5D6063908
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF- 2020R1F1A107746211

Revision History (Full details and data files)

Version 1.0: 2025-05-21
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.