8BA9

CryoEM structure of GroEL-GroES-ADP.AlF3-Rubisco.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis of substrate progression through the bacterial chaperonin cycle.

Gardner, S.Darrow, M.C.Lukoyanova, N.Thalassinos, K.Saibil, H.R.

(2023) Proc Natl Acad Sci U S A 120: e2308933120

  • DOI: https://doi.org/10.1073/pnas.2308933120
  • Primary Citation of Related Structures:  
    8BA7, 8BA8, 8BA9

  • PubMed Abstract: 

    The bacterial chaperonin GroEL-GroES promotes protein folding through ATP-regulated cycles of substrate protein binding, encapsulation, and release. Here, we have used cryoEM to determine structures of GroEL, GroEL-ADP·BeF 3 , and GroEL-ADP·AlF 3 -GroES all complexed with the model substrate Rubisco. Our structures provide a series of snapshots that show how the conformation and interactions of non-native Rubisco change as it proceeds through the GroEL-GroES reaction cycle. We observe specific charged and hydrophobic GroEL residues forming strong initial contacts with non-native Rubisco. Binding of ATP or ADP·BeF 3 to GroEL-Rubisco results in the formation of an intermediate GroEL complex displaying striking asymmetry in the ATP/ADP·BeF 3 -bound ring. In this ring, four GroEL subunits bind Rubisco and the other three are in the GroES-accepting conformation, suggesting how GroEL can recruit GroES without releasing bound substrate. Our cryoEM structures of stalled GroEL-ADP·AlF 3 -Rubisco-GroES complexes show Rubisco folding intermediates interacting with GroEL-GroES via different sets of residues.


  • Organizational Affiliation

    Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London WC1E 7HX, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60 kDa chaperonin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
524Escherichia coli K-12Mutation(s): 0 
Gene Names: groLgroELmopAb4143JW4103
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 GroES
O, P, Q, R, S
O, P, Q, R, S, T, U
97Escherichia coli K-12Mutation(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
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
CB [auth L]
DA [auth C]
FA [auth D]
HB [auth M]
JA [auth E]
CB [auth L],
DA [auth C],
FA [auth D],
HB [auth M],
JA [auth E],
JB [auth N],
LA [auth F],
PA [auth G],
QA [auth H],
VA [auth I],
W [auth A],
Y [auth B],
YA [auth J],
ZA [auth K]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
AF3
Query on AF3

Download Ideal Coordinates CCD File 
CA [auth C]
GA [auth D]
HA [auth E]
KA [auth F]
OA [auth G]
CA [auth C],
GA [auth D],
HA [auth E],
KA [auth F],
OA [auth G],
V [auth A],
Z [auth B]
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
K
Query on K

Download Ideal Coordinates CCD File 
BB [auth K]
DB [auth L]
FB [auth M]
IB [auth N]
SA [auth H]
BB [auth K],
DB [auth L],
FB [auth M],
IB [auth N],
SA [auth H],
UA [auth I],
WA [auth J]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth K]
BA [auth C]
EA [auth D]
EB [auth L]
AA [auth B],
AB [auth K],
BA [auth C],
EA [auth D],
EB [auth L],
GB [auth M],
IA [auth E],
KB [auth N],
MA [auth F],
NA [auth G],
RA [auth H],
TA [auth I],
X [auth A],
XA [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M009513/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release