Crystal structure of Cpn-rls in complex with ATP analogue from Methanococcus maripaludis

Experimental Data Snapshot

  • Resolution: 2.24 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Mechanism of nucleotide sensing in group II chaperonins.

Pereira, J.H.Ralston, C.Y.Douglas, N.R.Kumar, R.Lopez, T.McAndrew, R.P.Knee, K.M.King, J.A.Frydman, J.Adams, P.D.

(2012) EMBO J 31: 731-740

  • DOI: https://doi.org/10.1038/emboj.2011.468
  • Primary Citation of Related Structures:  
    3RUQ, 3RUS, 3RUV, 3RUW

  • PubMed Abstract: 

    Group II chaperonins mediate protein folding in an ATP-dependent manner in eukaryotes and archaea. The binding of ATP and subsequent hydrolysis promotes the closure of the multi-subunit rings where protein folding occurs. The mechanism by which local changes in the nucleotide-binding site are communicated between individual subunits is unknown. The crystal structure of the archaeal chaperonin from Methanococcus maripaludis in several nucleotides bound states reveals the local conformational changes associated with ATP hydrolysis. Residue Lys-161, which is extremely conserved among group II chaperonins, forms interactions with the γ-phosphate of ATP but shows a different orientation in the presence of ADP. The loss of the ATP γ-phosphate interaction with Lys-161 in the ADP state promotes a significant rearrangement of a loop consisting of residues 160-169. We propose that Lys-161 functions as an ATP sensor and that 160-169 constitutes a nucleotide-sensing loop (NSL) that monitors the presence of the γ-phosphate. Functional analysis using NSL mutants shows a significant decrease in ATPase activity, suggesting that the NSL is involved in timing of the protein folding cycle.

  • Organizational Affiliation

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
543Methanococcus maripaludisMutation(s): 4 
Find proteins for Q877G8 (Methanococcus maripaludis)
Explore Q877G8 
Go to UniProtKB:  Q877G8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ877G8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ANP

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
R [auth C],
X [auth D]
C10 H17 N6 O12 P3
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
G [auth A]
H [auth A]
I [auth A]
M [auth B]
AA [auth D],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
U [auth C],
Y [auth D],
Z [auth D]
O4 S
Query on MG

Download Ideal Coordinates CCD File 
BA [auth D]
E [auth A]
J [auth A]
K [auth B]
P [auth B]
BA [auth D],
E [auth A],
J [auth A],
K [auth B],
P [auth B],
Q [auth C],
V [auth C],
W [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.24 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.019α = 90
b = 184.477β = 90
c = 184.785γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-04
    Type: Initial release
  • Version 1.1: 2012-02-15
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description