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- PDB-9rwq: Ancestral Group III Chaperonin (ACIII) Double-Ring in Open Confor... -

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Basic information

Entry
Database: PDB / ID: 9rwq
TitleAncestral Group III Chaperonin (ACIII) Double-Ring in Open Conformation including the Equatorial and Intermediate Domains (residues 12-200 and 356-507)
ComponentsAncestral Group II Chaperonin (ACII)
KeywordsCHAPERONE / Chaperonins / Ancestors / Evolution / Cryoelectron Microscopy
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsCuellar, J. / Gutierrez-Seijo, J. / Severino, R.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2021-126746NB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2022-137175NB-I00 Spain
Other privateRTI2018-094368-B-I00
CitationJournal: Mol Biol Evol / Year: 2025
Title: Ancestral Chaperonins Provide the First Structural Glimpse into Early Multimeric Protein Evolution.
Authors: Rita Severino / Jorge Cuéllar / Jorge Gutiérrez-Seijo / Moisés Maestro-López / Luis Sánchez-Pulido / César Santiago / Mercedes Moreno-Paz / José María Valpuesta / Víctor Parro /
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 ...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.
History
DepositionJul 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Dec 24, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.1Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: Ancestral Group II Chaperonin (ACII)
A: Ancestral Group II Chaperonin (ACII)
B: Ancestral Group II Chaperonin (ACII)
C: Ancestral Group II Chaperonin (ACII)
D: Ancestral Group II Chaperonin (ACII)
E: Ancestral Group II Chaperonin (ACII)
F: Ancestral Group II Chaperonin (ACII)
G: Ancestral Group II Chaperonin (ACII)
H: Ancestral Group II Chaperonin (ACII)
I: Ancestral Group II Chaperonin (ACII)
J: Ancestral Group II Chaperonin (ACII)
K: Ancestral Group II Chaperonin (ACII)
L: Ancestral Group II Chaperonin (ACII)
M: Ancestral Group II Chaperonin (ACII)
O: Ancestral Group II Chaperonin (ACII)
P: Ancestral Group II Chaperonin (ACII)


Theoretical massNumber of molelcules
Total (without water)890,83216
Polymers890,83216
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Ancestral Group II Chaperonin (ACII)


Mass: 55676.984 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ancestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.889 MDa / Experimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 48 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1Xmipp3particle selection
2EPUimage acquisition
4Gctf3CTF correction
7Coot0.9.8.96model fitting
9RELION5initial Euler assignment
10cryoSPARC4initial Euler assignment
11cryoSPARC4final Euler assignment
12RELION5classification
13cryoSPARC43D reconstruction
14PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 504265
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40850 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00541328
ELECTRON MICROSCOPYf_angle_d0.91655968
ELECTRON MICROSCOPYf_dihedral_angle_d4.6475904
ELECTRON MICROSCOPYf_chiral_restr0.0466768
ELECTRON MICROSCOPYf_plane_restr0.0077504

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