9WCW | pdb_00009wcw

AMP-PNP bound E.coli CnoX-GroEL complex, state I

PDB DOI: https://doi.org/10.2210/pdb9WCW/pdb
EM Map EMD-65877: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-08-18 Released: 2026-08-05
Deposition Author(s): Kim, J., Roh, S.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.73 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural interplay of the redox co-chaperone CnoX to GroEL/ES chaperonin.

Kim, J., Jung, M., Roh, S.H.

(2026) Life Sci Alliance 9

PubMed: 42567683 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.26508/lsa.202603764
Primary Citation Related Structures:
9WCW, 9WID, 9WIE, 9WIF

PubMed Abstract:
Protein folding by the bacterial chaperonin GroEL/ES relies on ATP-driven conformational cycles that promote substrate encapsulation and folding. Under oxidative stress, the redox-active co-chaperone CnoX protects oxidized proteins and associates with GroEL, yet the structural basis of its interaction with the GroEL/ES remains incompletely understood. Using single-particle cryo-electron microscopy, we resolved four distinct nucleotide-bound conformational states of CnoX-associated GroEL/ES complexes. CnoX remains tethered to GroEL through its C-terminal TPR domain despite substantial rearrangements of the GroEL apical domains. We further captured a GroEL/ES-CnoX ternary assembly in which CnoX and GroES simultaneously occupy the same GroEL ring, demonstrating that their binding sites are structurally distinct and non-overlapping. Comparison of two GroES-bound states reveals how apical-domain compaction occludes the CnoX-binding surface and coincides with loss of CnoX from the cis-ring. Together, these structures define how CnoX is accommodated and excluded across distinct GroEL/ES conformations and provide a structural framework for understanding the interplay between redox co-chaperones and chaperonin assemblies.

Organizational Affiliation

School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.

Macromolecule Content

Total Structure Weight: 1,256.85 kDa
Atom Count: 64,078
Modeled Residue Count: 8,568
Deposited Residue Count: 11,648
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperedoxin	A B C D E A, B, C, D, E, F, L [auth M], N [auth O], P [auth Q], R [auth S], T [auth U], V [auth W], X [auth Y], Z [auth a]	284	Escherichia coli K-12	Mutation(s): 0 Gene Names: cnoX, ybbN, b0492, JW5067
UniProt
Find proteins for P77395 (Escherichia coli (strain K12)) Explore P77395 Go to UniProtKB: P77395
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P77395
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperonin GroEL	AA [auth b] BA [auth c] G H [auth I] I [auth J] AA [auth b], BA [auth c], G, H [auth I], I [auth J], J [auth K], K [auth L], M [auth N], O [auth P], Q [auth R], S [auth T], U [auth V], W [auth X], Y [auth Z]	548	Escherichia coli K-12	Mutation(s): 0 Gene Names: groEL, groL, mopA, b4143, JW4103 EC: 5.6.1.7
UniProt
Find proteins for P0A6F5 (Escherichia coli (strain K12)) Explore P0A6F5 Go to UniProtKB: P0A6F5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6F5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download:Ideal Coordinates CCD File SDF format, chain ZA [auth R] SDF format, chain WA [auth P] SDF format, chain RB [auth c] SDF format, chain RA [auth N] SDF format, chain QA [auth L] SDF format, chain OB [auth b] SDF format, chain LB [auth Z] SDF format, chain LA [auth K] SDF format, chain KA [auth J] SDF format, chain HB [auth X] SDF format, chain HA [auth I] SDF format, chain EB [auth V] SDF format, chain CB [auth T] SDF format, chain CA [auth G] MOL2 format, chain ZA [auth R] MOL2 format, chain WA [auth P] MOL2 format, chain RB [auth c] MOL2 format, chain RA [auth N] MOL2 format, chain QA [auth L] MOL2 format, chain OB [auth b] MOL2 format, chain LB [auth Z] MOL2 format, chain LA [auth K] MOL2 format, chain KA [auth J] MOL2 format, chain HB [auth X] MOL2 format, chain HA [auth I] MOL2 format, chain EB [auth V] MOL2 format, chain CB [auth T] MOL2 format, chain CA [auth G] mmCIF format, chain ZA [auth R] mmCIF format, chain WA [auth P] mmCIF format, chain RB [auth c] mmCIF format, chain RA [auth N] mmCIF format, chain QA [auth L] mmCIF format, chain OB [auth b] mmCIF format, chain LB [auth Z] mmCIF format, chain LA [auth K] mmCIF format, chain KA [auth J] mmCIF format, chain HB [auth X] mmCIF format, chain HA [auth I] mmCIF format, chain EB [auth V] mmCIF format, chain CB [auth T] mmCIF format, chain CA [auth G]	CA [auth G] CB [auth T] EB [auth V] HA [auth I] HB [auth X] CA [auth G], CB [auth T], EB [auth V], HA [auth I], HB [auth X], KA [auth J], LA [auth K], LB [auth Z], OB [auth b], QA [auth L], RA [auth N], RB [auth c], WA [auth P], ZA [auth R]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain CA [auth G] Focus chain CB [auth T] Focus chain EB [auth V] Focus chain HA [auth I] Focus chain HB [auth X] Focus chain KA [auth J] Focus chain LA [auth K] Focus chain LB [auth Z] Focus chain OB [auth b] Focus chain QA [auth L] Focus chain RA [auth N] Focus chain RB [auth c] Focus chain WA [auth P] Focus chain ZA [auth R] Interactions & Density Focus chain CA [auth G] Focus chain CB [auth T] Focus chain EB [auth V] Focus chain HA [auth I] Focus chain HB [auth X] Focus chain KA [auth J] Focus chain LA [auth K] Focus chain LB [auth Z] Focus chain OB [auth b] Focus chain QA [auth L] Focus chain RA [auth N] Focus chain RB [auth c] Focus chain WA [auth P] Focus chain ZA [auth R]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain YA [auth R] SDF format, chain VA [auth P] SDF format, chain SA [auth N] SDF format, chain QB [auth c] SDF format, chain OA [auth L] SDF format, chain NB [auth b] SDF format, chain NA [auth K] SDF format, chain KB [auth Z] SDF format, chain IA [auth J] SDF format, chain GB [auth X] SDF format, chain GA [auth I] SDF format, chain EA [auth G] SDF format, chain DB [auth V] SDF format, chain AB [auth T] MOL2 format, chain YA [auth R] MOL2 format, chain VA [auth P] MOL2 format, chain SA [auth N] MOL2 format, chain QB [auth c] MOL2 format, chain OA [auth L] MOL2 format, chain NB [auth b] MOL2 format, chain NA [auth K] MOL2 format, chain KB [auth Z] MOL2 format, chain IA [auth J] MOL2 format, chain GB [auth X] MOL2 format, chain GA [auth I] MOL2 format, chain EA [auth G] MOL2 format, chain DB [auth V] MOL2 format, chain AB [auth T] mmCIF format, chain YA [auth R] mmCIF format, chain VA [auth P] mmCIF format, chain SA [auth N] mmCIF format, chain QB [auth c] mmCIF format, chain OA [auth L] mmCIF format, chain NB [auth b] mmCIF format, chain NA [auth K] mmCIF format, chain KB [auth Z] mmCIF format, chain IA [auth J] mmCIF format, chain GB [auth X] mmCIF format, chain GA [auth I] mmCIF format, chain EA [auth G] mmCIF format, chain DB [auth V] mmCIF format, chain AB [auth T]	AB [auth T] DB [auth V] EA [auth G] GA [auth I] GB [auth X] AB [auth T], DB [auth V], EA [auth G], GA [auth I], GB [auth X], IA [auth J], KB [auth Z], NA [auth K], NB [auth b], OA [auth L], QB [auth c], SA [auth N], VA [auth P], YA [auth R]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AB [auth T] Focus chain DB [auth V] Focus chain EA [auth G] Focus chain GA [auth I] Focus chain GB [auth X] Focus chain IA [auth J] Focus chain KB [auth Z] Focus chain NA [auth K] Focus chain NB [auth b] Focus chain OA [auth L] Focus chain QB [auth c] Focus chain SA [auth N] Focus chain VA [auth P] Focus chain YA [auth R] Interactions & Density Focus chain AB [auth T] Focus chain DB [auth V] Focus chain EA [auth G] Focus chain GA [auth I] Focus chain GB [auth X] Focus chain IA [auth J] Focus chain KB [auth Z] Focus chain NA [auth K] Focus chain NB [auth b] Focus chain OA [auth L] Focus chain QB [auth c] Focus chain SA [auth N] Focus chain VA [auth P] Focus chain YA [auth R]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain XA [auth R] SDF format, chain UA [auth P] SDF format, chain TA [auth N] SDF format, chain PB [auth c] SDF format, chain PA [auth L] SDF format, chain MB [auth b] SDF format, chain MA [auth K] SDF format, chain JB [auth Z] SDF format, chain JA [auth J] SDF format, chain IB [auth X] SDF format, chain FB [auth V] SDF format, chain FA [auth I] SDF format, chain DA [auth G] SDF format, chain BB [auth T] MOL2 format, chain XA [auth R] MOL2 format, chain UA [auth P] MOL2 format, chain TA [auth N] MOL2 format, chain PB [auth c] MOL2 format, chain PA [auth L] MOL2 format, chain MB [auth b] MOL2 format, chain MA [auth K] MOL2 format, chain JB [auth Z] MOL2 format, chain JA [auth J] MOL2 format, chain IB [auth X] MOL2 format, chain FB [auth V] MOL2 format, chain FA [auth I] MOL2 format, chain DA [auth G] MOL2 format, chain BB [auth T] mmCIF format, chain XA [auth R] mmCIF format, chain UA [auth P] mmCIF format, chain TA [auth N] mmCIF format, chain PB [auth c] mmCIF format, chain PA [auth L] mmCIF format, chain MB [auth b] mmCIF format, chain MA [auth K] mmCIF format, chain JB [auth Z] mmCIF format, chain JA [auth J] mmCIF format, chain IB [auth X] mmCIF format, chain FB [auth V] mmCIF format, chain FA [auth I] mmCIF format, chain DA [auth G] mmCIF format, chain BB [auth T]	BB [auth T] DA [auth G] FA [auth I] FB [auth V] IB [auth X] BB [auth T], DA [auth G], FA [auth I], FB [auth V], IB [auth X], JA [auth J], JB [auth Z], MA [auth K], MB [auth b], PA [auth L], PB [auth c], TA [auth N], UA [auth P], XA [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BB [auth T] Focus chain DA [auth G] Focus chain FA [auth I] Focus chain FB [auth V] Focus chain IB [auth X] Focus chain JA [auth J] Focus chain JB [auth Z] Focus chain MA [auth K] Focus chain MB [auth b] Focus chain PA [auth L] Focus chain PB [auth c] Focus chain TA [auth N] Focus chain UA [auth P] Focus chain XA [auth R] Interactions & Density Focus chain BB [auth T] Focus chain DA [auth G] Focus chain FA [auth I] Focus chain FB [auth V] Focus chain IB [auth X] Focus chain JA [auth J] Focus chain JB [auth Z] Focus chain MA [auth K] Focus chain MB [auth b] Focus chain PA [auth L] Focus chain PB [auth c] Focus chain TA [auth N] Focus chain UA [auth P] Focus chain XA [auth R]