[English] 日本語
Yorodumi
- EMDB-54341: Ancestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54341
TitleAncestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB) Double-Ring in Open Conformation
Map dataAncestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB) Double-Ring in Open Conformation
Sample
  • Complex: Ancestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB)
    • Protein or peptide: Ancestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB)
KeywordsChaperonins / Ancestors / Evolution / Cryoelectron Microscopy / CHAPERONE
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 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

-
Structure visualization

Supplemental images

emd_54341.png

Downloads & links

-
Map

FileDownload / File: emd_54341.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAncestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB) Double-Ring in Open Conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 260 pix.
= 307.788 Å		1.18 Å/pix.
x 260 pix.
= 307.788 Å		1.18 Å/pix.
x 260 pix.
= 307.788 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1838 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-0.0018977025 - 2.0331275
Average (Standard dev.)0.0055305837 (±0.05603248)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 307.788 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_54341_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_54341_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_54341_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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 Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB)

-
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: 802 KDa

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

MacromoleculeName: Ancestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB)
type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 56.053145 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AKQIKFDTDA RNALLRGVDK LADAVKVTLG PKGRNVIIEK KFGAPTITKD GVTVAKEIEL EDPFENMGAQ MVKEVASKTS DVAGDGTTT ATVLAQAIVR EGLKNVAAGA NPMDLKRGID KAVEAVVEEL KKMAKPVNGK EEIAQVATIS ANNDPEIGKL I AEAMEKVG ...String:
AKQIKFDTDA RNALLRGVDK LADAVKVTLG PKGRNVIIEK KFGAPTITKD GVTVAKEIEL EDPFENMGAQ MVKEVASKTS DVAGDGTTT ATVLAQAIVR EGLKNVAAGA NPMDLKRGID KAVEAVVEEL KKMAKPVNGK EEIAQVATIS ANNDPEIGKL I AEAMEKVG KDGVITVEES KSTETTLDVV EGMQFDRGYL SPYFVTDSEK MEAVLENPYI LIYDKKISNM KDLLPILEKV AQ SGKPLLI IAEDVEGEAL ATLVVNKLRG TLKVCAVKAP GFGDRRKAML EDIAILTGGT VISEETGYKL ENATLDYLGR AKR VTIDKD NTTIVDGAGD KEDIKARVNQ IKKQIENTTS DYDREKLQER LAKLAGGVAV IKVGAATEVE MKEKKARVED ALHA TRAAV EEGIVPGGGV ALIRAAKALE NLEGENGDQK TGVKIVRRAL EEPLRQIVAN AGLEGSVVVN KVKEGKGNFG YNART EEYD LIEAGVIDPA KVTRTALQNA ASIAGMLLTT ECVITEKP

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 43.0 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

+
Image processing

Particle selectionNumber selected: 245876
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: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 44531
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)

-
Atomic model buiding 1

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

PDB-9rwr:
Ancestral Fibrobacteres-Chlorobi-Bacteroidetes Group Chaperonin (AFCB) Double-Ring in Open Conformation

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more