9RWP | pdb_00009rwp

Ancestral Group II Chaperonin (ACII) Double-Ring in Closed Conformation

PDB DOI: https://doi.org/10.2210/pdb9RWP/pdb
EM Map EMD-54339: 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

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.69 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

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 Search on PubMed
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.

Organizational Affiliation

Centro de Astrobiología (CAB), INTA-CSIC, Torrejón de Ardoz, Madrid, Spain.

Macromolecule Content

Total Structure Weight: 916.21 kDa
Atom Count: 59,888
Modeled Residue Count: 7,936
Deposited Residue Count: 8,480
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ancestral Group II Chaperonin (ACII)	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	530	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain CA [auth G] SDF format, chain EA [auth H] SDF format, chain GA [auth I] SDF format, chain IA [auth J] SDF format, chain KA [auth K] SDF format, chain MA [auth L] SDF format, chain OA [auth M] SDF format, chain Q [auth A] SDF format, chain QA [auth N] SDF format, chain S [auth B] SDF format, chain SA [auth O] SDF format, chain U [auth C] SDF format, chain UA [auth P] SDF format, chain W [auth D] SDF format, chain Y [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain IA [auth J] MOL2 format, chain KA [auth K] MOL2 format, chain MA [auth L] MOL2 format, chain OA [auth M] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth N] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth O] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth P] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain GA [auth I] mmCIF format, chain IA [auth J] mmCIF format, chain KA [auth K] mmCIF format, chain MA [auth L] mmCIF format, chain OA [auth M] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth N] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth O] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth P] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth E]	AA [auth F] CA [auth G] EA [auth H] GA [auth I] IA [auth J] AA [auth F], CA [auth G], EA [auth H], GA [auth I], IA [auth J], KA [auth K], MA [auth L], OA [auth M], Q [auth A], QA [auth N], S [auth B], SA [auth O], U [auth C], UA [auth P], W [auth D], Y [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain IA [auth J] Focus chain KA [auth K] Focus chain MA [auth L] Focus chain OA [auth M] Focus chain Q [auth A] Focus chain QA [auth N] Focus chain S [auth B] Focus chain SA [auth O] Focus chain U [auth C] Focus chain UA [auth P] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain IA [auth J] Focus chain KA [auth K] Focus chain MA [auth L] Focus chain OA [auth M] Focus chain Q [auth A] Focus chain QA [auth N] Focus chain S [auth B] Focus chain SA [auth O] Focus chain U [auth C] Focus chain UA [auth P] Focus chain W [auth D] Focus chain Y [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain DA [auth G] SDF format, chain FA [auth H] SDF format, chain HA [auth I] SDF format, chain JA [auth J] SDF format, chain LA [auth K] SDF format, chain NA [auth L] SDF format, chain PA [auth M] SDF format, chain R [auth A] SDF format, chain RA [auth N] SDF format, chain T [auth B] SDF format, chain TA [auth O] SDF format, chain V [auth C] SDF format, chain VA [auth P] SDF format, chain X [auth D] SDF format, chain Z [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain HA [auth I] MOL2 format, chain JA [auth J] MOL2 format, chain LA [auth K] MOL2 format, chain NA [auth L] MOL2 format, chain PA [auth M] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth N] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth O] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth P] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain HA [auth I] mmCIF format, chain JA [auth J] mmCIF format, chain LA [auth K] mmCIF format, chain NA [auth L] mmCIF format, chain PA [auth M] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth N] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth O] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth P] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E]	BA [auth F] DA [auth G] FA [auth H] HA [auth I] JA [auth J] BA [auth F], DA [auth G], FA [auth H], HA [auth I], JA [auth J], LA [auth K], NA [auth L], PA [auth M], R [auth A], RA [auth N], T [auth B], TA [auth O], V [auth C], VA [auth P], X [auth D], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain JA [auth J] Focus chain LA [auth K] Focus chain NA [auth L] Focus chain PA [auth M] Focus chain R [auth A] Focus chain RA [auth N] Focus chain T [auth B] Focus chain TA [auth O] Focus chain V [auth C] Focus chain VA [auth P] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain JA [auth J] Focus chain LA [auth K] Focus chain NA [auth L] Focus chain PA [auth M] Focus chain R [auth A] Focus chain RA [auth N] Focus chain T [auth B] Focus chain TA [auth O] Focus chain V [auth C] Focus chain VA [auth P] Focus chain X [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.69 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-10

Deposition Author(s):

Cuellar, J.

Gutierrez-Seijo, J.

Severino, R.

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