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- PDB-9rwp: Ancestral Group II Chaperonin (ACII) Double-Ring in Closed Confor... -

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Basic information

Entry
Database: PDB / ID: 9rwp
TitleAncestral Group II Chaperonin (ACII) Double-Ring in Closed Conformation
ComponentsAncestral Group II Chaperonin (ACII)
KeywordsCHAPERONE / Chaperonins / Ancestors / Evolution / Cryoelectron Microscopy
Function / homologyADENOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.69 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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)
N: Ancestral Group II Chaperonin (ACII)
O: Ancestral Group II Chaperonin (ACII)
P: Ancestral Group II Chaperonin (ACII)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)916,20648
Polymers908,98216
Non-polymers7,22432
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: 56811.383 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)
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
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 Group II Chaperonin (ACII) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.908 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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 38 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1Xmipp3particle selection
2PHENIX1.20.1_4487:model refinement
5Gctf3CTF correction
10cryoSPARC4initial Euler assignment
11RELION5initial Euler assignment
12cryoSPARC4final Euler assignment
13RELION5classification
14cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2474620
SymmetryPoint symmetry: D8 (2x8 fold dihedral)
3D reconstructionResolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39180 / 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_d0.00560384
ELECTRON MICROSCOPYf_angle_d0.89681616
ELECTRON MICROSCOPYf_dihedral_angle_d8.458448
ELECTRON MICROSCOPYf_chiral_restr0.0499824
ELECTRON MICROSCOPYf_plane_restr0.00610704

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