9RWQ | pdb_00009rwq

Ancestral Group III Chaperonin (ACIII) Double-Ring in Open Conformation including the Equatorial and Intermediate Domains (residues 12-200 and 356-507)

• PDB DOI: https://doi.org/10.2210/pdb9RWQ/pdb
• EM Map EMD-54340: EMDB EMDataResource

• Classification: CHAPERONE
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-07-09 Released: 2025-12-10 
• Deposition Author(s): Cuellar, J., Gutierrez-Seijo, J., Severino, R.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities, Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Ancestral Chaperonins Provide the First Structural Glimpse into Early Multimeric Protein Evolution.

Severino, R., Cuellar, J., Gutierrez-Seijo, J., Maestro-Lopez, M., Sanchez-Pulido, L., Santiago, C., Moreno-Paz, M., Valpuesta, J.M., Parro, V.

(2025) Mol Biol Evol 

• PubMed: 41310978 
• DOI: https://doi.org/10.1093/molbev/msaf314
• Primary Citation of Related Structures:  
  9RWP, 9RWQ, 9RWR


• PubMed Abstract: 
  

  Chaperonins are essential protein-folding machines, classified into three structural and phylogenetic groups: Group I (bacterial GroEL), Group II (archaeal thermosome and eukaryotic CCT), and Group III (bacterial thermosome-like). Using ancestral sequence reconstruction (ASR) and protein resurrection, we inferred and experimentally characterized the last common ancestors of these groups (Ancestral Chaperonins ACI, ACII, and ACIII). The resurrected proteins exhibited ATPase activity (except ACII) and protected client proteins from heat-induced inactivation. Structural analyses by electron microscopy and Cryo-EM revealed that ACI forms single 7-mer rings, whereas ACII adopts a mixed population of single/double 8-mer rings, representing the first experimental observation of intermediate oligomeric states. ACII also features a unique cochaperonin-independent closure mechanism, distinct from modern Group I and II chaperonins. Together, these findings provide the experimental structural reconstruction of the most ancient and complex multimeric proteins so far, uncover novel intermediate states in chaperonin evolution, and offer a direct empirical framework for studying the emergence of multimeric complexity in early cellular life.

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Organizational Affiliation: 
• Centro de Astrobiología (CAB), INTA-CSIC, Torrejón de Ardoz, Madrid, Spain.
University of Alcalá (UAH), Alcalá de Henares, Madrid, Spain.
National Center for Biotechnology (CNB), CSIC, Madrid, Spain.
Unidad de Nanobiotecnología, CNB-CSIC-IMDEA Nanociencia Associated Unit, Madrid, Spain.

Biological Assembly 1  

Global Symmetry: Dihedral - D8  (Explore in 3D)
Global Stoichiometry: Homo 16-mer - A16 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 890.83 kDa 
• Atom Count: 40,496 
• Modeled Residue Count: 5,456 
• Deposited Residue Count: 8,288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ancestral Group II Chaperonin (ACII)	A [auth N], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K], M [auth L], N [auth M], O, P	518	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.0
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Cuellar, J., Gutierrez-Seijo, J., Severino, R.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2021-126746NB-I00
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2022-137175NB-I00
Other private		RTI2018-094368-B-I00

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release