5OPX

Crystal structure of the GroEL mutant A109C in complex with GroES and ADP BeF2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.64 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

GroEL Ring Separation and Exchange in the Chaperonin Reaction.

Yan, X.Shi, Q.Bracher, A.Milicic, G.Singh, A.K.Hartl, F.U.Hayer-Hartl, M.

(2018) Cell 172: 605-617.e11

  • DOI: https://doi.org/10.1016/j.cell.2017.12.010
  • Primary Citation of Related Structures:  
    5OPW, 5OPX

  • PubMed Abstract: 

    The bacterial chaperonin GroEL and its cofactor, GroES, form a nano-cage for a single molecule of substrate protein (SP) to fold in isolation. GroEL and GroES undergo an ATP-regulated interaction cycle to close and open the folding cage. GroEL consists of two heptameric rings stacked back to back. Here, we show that GroEL undergoes transient ring separation, resulting in ring exchange between complexes. Ring separation occurs upon ATP-binding to the trans ring of the asymmetric GroEL:7ADP:GroES complex in the presence or absence of SP and is a consequence of inter-ring negative allostery. We find that a GroEL mutant unable to perform ring separation is folding active but populates symmetric GroEL:GroES 2 complexes, where both GroEL rings function simultaneously rather than sequentially. As a consequence, SP binding and release from the folding chamber is inefficient, and E. coli growth is impaired. We suggest that transient ring separation is an integral part of the chaperonin mechanism.


  • Organizational Affiliation

    Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.


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
548Escherichia coli K-12Mutation(s): 1 
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
10 kDa chaperonin97Escherichia coli K-12Mutation(s): 0 
Gene Names: groSgroESmopBb4142JW4102
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 
AB [auth G]
CA [auth A]
CC [auth N]
EB [auth H]
GA [auth B]
AB [auth G],
CA [auth A],
CC [auth N],
EB [auth H],
GA [auth B],
IB [auth I],
KA [auth C],
MB [auth J],
OA [auth D],
QB [auth K],
SA [auth E],
UB [auth L],
WA [auth F],
YB [auth M]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF
Query on BEF

Download Ideal Coordinates CCD File 
AC [auth M]
CB [auth G]
EA [auth A]
EC [auth N]
GB [auth H]
AC [auth M],
CB [auth G],
EA [auth A],
EC [auth N],
GB [auth H],
IA [auth B],
KB [auth I],
MA [auth C],
OB [auth J],
QA [auth D],
SB [auth K],
UA [auth E],
WB [auth L],
YA [auth F]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
K
Query on K

Download Ideal Coordinates CCD File 
BC [auth M]
DB [auth G]
FA [auth A]
FC [auth N]
HB [auth H]
BC [auth M],
DB [auth G],
FA [auth A],
FC [auth N],
HB [auth H],
JA [auth B],
LB [auth I],
NA [auth C],
PB [auth J],
RA [auth D],
TB [auth K],
VA [auth E],
XB [auth L],
ZA [auth F]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BB [auth G]
DA [auth A]
DC [auth N]
FB [auth H]
HA [auth B]
BB [auth G],
DA [auth A],
DC [auth N],
FB [auth H],
HA [auth B],
JB [auth I],
LA [auth C],
NB [auth J],
PA [auth D],
RB [auth K],
TA [auth E],
VB [auth L],
XA [auth F],
ZB [auth M]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.64 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 217.567α = 90
b = 230.504β = 90
c = 235.391γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2018-02-07
    Changes: Database references
  • Version 1.3: 2019-05-08
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description