8P4O

CryoEM structure of a GroEL7-GroES7 cage with encapsulated ordered substrate MetK in the presence of ADP-BeFx


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Visualizing chaperonin function in situ by cryo-electron tomography.

Wagner, J.Carvajal, A.I.Bracher, A.Beck, F.Wan, W.Bohn, S.Korner, R.Baumeister, W.Fernandez-Busnadiego, R.Hartl, F.U.

(2024) Nature 633: 459-464

  • DOI: https://doi.org/10.1038/s41586-024-07843-w
  • Primary Citation of Related Structures:  
    8P4M, 8P4N, 8P4O, 8P4P, 8P4R, 8QXS, 8QXT, 8QXU, 8QXV

  • PubMed Abstract: 

    Chaperonins are large barrel-shaped complexes that mediate ATP-dependent protein folding 1-3 . The bacterial chaperonin GroEL forms juxtaposed rings that bind unfolded protein and the lid-shaped cofactor GroES at their apertures. In vitro analyses of the chaperonin reaction have shown that substrate protein folds, unimpaired by aggregation, while transiently encapsulated in the GroEL central cavity by GroES 4-6 . To determine the functional stoichiometry of GroEL, GroES and client protein in situ, here we visualized chaperonin complexes in their natural cellular environment using cryo-electron tomography. We find that, under various growth conditions, around 55-70% of GroEL binds GroES asymmetrically on one ring, with the remainder populating symmetrical complexes. Bound substrate protein is detected on the free ring of the asymmetrical complex, defining the substrate acceptor state. In situ analysis of GroEL-GroES chambers, validated by high-resolution structures obtained in vitro, showed the presence of encapsulated substrate protein in a folded state before release into the cytosol. Based on a comprehensive quantification and conformational analysis of chaperonin complexes, we propose a GroEL-GroES reaction cycle that consists of linked asymmetrical and symmetrical subreactions mediating protein folding. Our findings illuminate the native conformational and functional chaperonin cycle directly within cells.


  • Organizational Affiliation

    Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperonin GroEL
A, B, C, D, E
A, B, C, D, E, F, G
547Escherichia coliMutation(s): 0 
Gene Names: groELgroLmopAb4143JW4103
EC: 5.6.1.7
UniProt
Find proteins for P0A6F5 (Escherichia coli (strain K12))
Explore P0A6F5 
Go to UniProtKB:  P0A6F5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6F5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Co-chaperonin GroES97Escherichia coliMutation(s): 0 
Gene Names: groESgroSmopBb4142JW4102
UniProt
Find proteins for P0A6F9 (Escherichia coli (strain K12))
Explore P0A6F9 
Go to UniProtKB:  P0A6F9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6F9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
S-adenosylmethionine synthaseO [auth 1]384Escherichia coliMutation(s): 0 
Gene Names: metKmetXb2942JW2909
EC: 2.5.1.6
UniProt
Find proteins for P0A817 (Escherichia coli (strain K12))
Explore P0A817 
Go to UniProtKB:  P0A817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A817
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth D]
FA [auth E]
JA [auth F]
NA [auth G]
P [auth A]
BA [auth D],
FA [auth E],
JA [auth F],
NA [auth G],
P [auth A],
T [auth B],
X [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF
Query on BEF

Download Ideal Coordinates CCD File 
DA [auth D]
HA [auth E]
LA [auth F]
PA [auth G]
R [auth A]
DA [auth D],
HA [auth E],
LA [auth F],
PA [auth G],
R [auth A],
V [auth B],
Z [auth C]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth C]
EA [auth D]
IA [auth E]
MA [auth F]
QA [auth G]
AA [auth C],
EA [auth D],
IA [auth E],
MA [auth F],
QA [auth G],
S [auth A],
W [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth D]
GA [auth E]
KA [auth F]
OA [auth G]
Q [auth A]
CA [auth D],
GA [auth E],
KA [auth F],
OA [auth G],
Q [auth A],
U [auth B],
Y [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2024-09-04
    Changes: Data collection, Database references
  • Version 1.3: 2024-09-25
    Changes: Data collection, Database references