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- EMDB-54339: Ancestral Group II Chaperonin (ACII) Double-Ring in Closed Confor... -

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Entry
Database: EMDB / ID: EMD-54339
TitleAncestral Group II Chaperonin (ACII) Double-Ring in Closed Conformation
Map dataAncestral Group II Chaperonin (ACII) Double-Ring in Closed Conformation
Sample
  • Complex: Ancestral Group II Chaperonin (ACII)
    • Protein or peptide: Ancestral Group II Chaperonin (ACII)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsChaperonins / Ancestors / Evolution / Cryoelectron Microscopy / CHAPERONE
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsCuellar J / Gutierrez-Seijo J / Severino R / Maestro-Lopez M / Sanchez-Pulido L / Santiago C / Moreno-Paz M / Valpuesta JM / Parro V
Funding support Spain, 3 items
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, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54339.png

Downloads & links

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Map

FileDownload / File: emd_54339.map.gz / Format: CCP4 / Size: 506 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAncestral Group II Chaperonin (ACII) Double-Ring in Closed Conformation
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 510 pix.
= 430.95 Å		0.85 Å/pix.
x 510 pix.
= 430.95 Å		0.85 Å/pix.
x 510 pix.
= 430.95 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.845 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0167
Minimum - Maximum-0.0018580685 - 2.0403383
Average (Standard dev.)0.0015176892 (±0.027646836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions510510510
Spacing510510510
CellA=B=C: 430.95 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54339_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54339_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Ancestral Group II Chaperonin (ACII)

EntireName: Ancestral Group II Chaperonin (ACII)
Components
  • Complex: Ancestral Group II Chaperonin (ACII)
    • Protein or peptide: Ancestral Group II Chaperonin (ACII)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Ancestral Group II Chaperonin (ACII)

SupramoleculeName: Ancestral Group II Chaperonin (ACII) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 908 KDa

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Macromolecule #1: Ancestral Group II Chaperonin (ACII)

MacromoleculeName: Ancestral Group II Chaperonin (ACII) / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 56.811383 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGQPMVVLSE NTERTSGRDA RKNNIAAARA IADMVKTTLG PRGMNKMLVN SLGDVTITND GATILEEMDI EHPAAKMLKE VAKAQEEEA GDGTTTAVVL AGALLEEAEK LIEQGIHPTT IIKGYRKAVD KALEVLEEVA IPVDPDDEET LKAVARTAMT G KASEENRE ...String:
MGQPMVVLSE NTERTSGRDA RKNNIAAARA IADMVKTTLG PRGMNKMLVN SLGDVTITND GATILEEMDI EHPAAKMLKE VAKAQEEEA GDGTTTAVVL AGALLEEAEK LIEQGIHPTT IIKGYRKAVD KALEVLEEVA IPVDPDDEET LKAVARTAMT G KASEENRE EIADLVVEAV LSLAEDGGGK YRVDLDNIKI EKQTGGGASD TELIEGVVLD KEPVHEDMPK KLENAKVAVL DA PIEVEKT ELDAKISISS PEQFQAFLDQ EEKQLREMVD KIVDTGANVV FCEKGIDDQV EHMLAKKGIL AVRRVKKDDL EKI AKATGA RVVSNIDELT PEDLGHAGLV EQRKKGEDRM VFVSGCKNEP VATILIRAAT EHVVEELERA IDDALNAVKA AIKD GKVVP GGGAAEVAVA RKLREYAKSL SGKEQLAIEA FADALEEIPR TLAENAGLDP IDTLVQLRAA HEEGDKNIGI DCLTG EVAD MLEAGVIDPA AVKKQAIKSA TEAATMILRI DDIIPAKAPT GEDGDG

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 16 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 16 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2474620
CTF correctionSoftware - Name: Gctf (ver. 3.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: CryoSparc Initial Model
Final reconstructionApplied symmetry - Point group: D8 (2x8 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 39180
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: cryoSPARC (ver. 4.0), RELION (ver. 5.0))
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: AB INITIO MODEL
Output model

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

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