3KFK | pdb_00003kfk

Crystal structures of a group II chaperonin from Methanococcus maripaludis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • R-Value Free: 
    0.270 (Depositor), 0.337 (DCC) 
  • R-Value Work: 
    0.241 (Depositor) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle.

Pereira, J.H.Ralston, C.Y.Douglas, N.R.Meyer, D.Knee, K.M.Goulet, D.R.King, J.A.Frydman, J.Adams, P.D.

(2010) J Biological Chem 285: 27958-27966

  • DOI: https://doi.org/10.1074/jbc.M110.125344
  • Primary Citation Related Structures: 
    3KFB, 3KFE, 3KFK

  • PubMed Abstract: 

    Chaperonins are large protein complexes consisting of two stacked multisubunit rings, which open and close in an ATP-dependent manner to create a protected environment for protein folding. Here, we describe the first crystal structure of a group II chaperonin in an open conformation. We have obtained structures of the archaeal chaperonin from Methanococcus maripaludis in both a peptide acceptor (open) state and a protein folding (closed) state. In contrast with group I chaperonins, in which the equatorial domains share a similar conformation between the open and closed states and the largest motions occurs at the intermediate and apical domains, the three domains of the archaeal chaperonin subunit reorient as a single rigid body. The large rotation observed from the open state to the closed state results in a 65% decrease of the folding chamber volume and creates a highly hydrophilic surface inside the cage. These results suggest a completely distinct closing mechanism in the group II chaperonins as compared with the group I chaperonins.


  • Organizational Affiliation
    • Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

Macromolecule Content 

  • Total Structure Weight: 224.55 kDa 
  • Atom Count: 14,619 
  • Modeled Residue Count: 1,945 
  • Deposited Residue Count: 2,084 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chaperonin
A, B, C, D
521Methanococcus maripaludisMutation(s): 4 
Gene Names: hsp60MMP1515
EC: 3.6.1 (UniProt), 5.6.1.7 (UniProt)
UniProt
Find proteins for Q6LX38 (Methanococcus maripaludis (strain DSM 14266 / JCM 13030 / NBRC 101832 / S2 / LL))
Explore Q6LX38 
Go to UniProtKB:  Q6LX38
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6LX38
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • R-Value Free:  0.270 (Depositor), 0.337 (DCC) 
  • R-Value Work:  0.241 (Depositor) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.533α = 90
b = 209.527β = 90
c = 266.862γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary