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- EMDB-54340: Ancestral Group III Chaperonin (ACIII) Double-Ring in Open Confor... -

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Entry
Database: EMDB / ID: EMD-54340
TitleAncestral Group III Chaperonin (ACIII) Double-Ring in Open Conformation including the Equatorial and Intermediate Domains (residues 12-200 and 356-507)
Map dataAncestral Group III Chaperonin (ACIII) Double Ring in Open Conformation
Sample
  • Complex: Ancestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB)
    • Protein or peptide: Ancestral Group II Chaperonin (ACII)
KeywordsChaperonins / Ancestors / Evolution / Cryoelectron Microscopy / CHAPERONE
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 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_54340.png

Downloads & links

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Map

FileDownload / File: emd_54340.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAncestral Group III Chaperonin (ACIII) Double Ring in Open Conformation
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 360 pix.
= 331.56 Å		0.92 Å/pix.
x 360 pix.
= 331.56 Å		0.92 Å/pix.
x 360 pix.
= 331.56 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.921 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0387
Minimum - Maximum-0.0018002397 - 1.8866999
Average (Standard dev.)0.0029345877 (±0.039983828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 331.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54340_msk_1.map
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Half map: #2

Fileemd_54340_half_map_1.map
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Half map: #1

Fileemd_54340_half_map_2.map
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Sample components

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Entire : Ancestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB)

EntireName: Ancestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB)
Components
  • Complex: Ancestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB)
    • Protein or peptide: Ancestral Group II Chaperonin (ACII)

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Supramolecule #1: Ancestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB)

SupramoleculeName: Ancestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 889 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: 55.676984 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPLKQASSNT EADERFQALL TNVNAVRAIA DAVEGTLGPK GLDVMLVDKF GEVTITNDGV TILDQMDVQH PAARMLIQVA RAQEEEVGD GTTTATVLAG ALVSEGVNQV EQGVPVSRVI EGLRRGVERA LELLRKQALP VEGLDDPRLR AVARIAARER E DIADLVVE ...String:
MPLKQASSNT EADERFQALL TNVNAVRAIA DAVEGTLGPK GLDVMLVDKF GEVTITNDGV TILDQMDVQH PAARMLIQVA RAQEEEVGD GTTTATVLAG ALVSEGVNQV EQGVPVSRVI EGLRRGVERA LELLRKQALP VEGLDDPRLR AVARIAARER E DIADLVVE AARHIGEDKL QDPNFKLADT VTAREGAENQ VIEGVVLNKQ PLNKEMPKKL EDARVLVLDD PLEPEEIDEE AL STEAGFA RYLEAQEEFR ENLEKLVELG VKLVLCEKGI DDTAEELLAE AGIMAIQRVS RKDLERVAEF TGARPVKRTA LNK DAEELA KLLGHAERVR YDEKLEHVCL SGGSGEPIAT VLVGAATEEV VGERERVAKD AASAVQAAIR GGVVPGGGAA ELAV AREVE KLAEEVKGME RYGVEAVAEA LKKPLRQIVA NAGFNPLEKL GDLRAAHRTG NDSLGIDCDT GEVVDMWEAG VIDPA PVKL HALKAAGEVA AAILRINTII KMKETGPDGG EDRG

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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

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 504265
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 40850
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION (ver. 5.0), cryoSPARC (ver. 4.0))
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
SoftwareName: Coot (ver. 0.9.8.96)
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9rwq:
Ancestral Group III Chaperonin (ACIII) Double-Ring in Open Conformation including the Equatorial and Intermediate Domains (residues 12-200 and 356-507)

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