3KFE | pdb_00003kfe

Crystal structures of a group II chaperonin from Methanococcus maripaludis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.269 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

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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: 449.29 kDa 
  • Atom Count: 29,296 
  • Modeled Residue Count: 3,896 
  • Deposited Residue Count: 4,168 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chaperonin
A, B, C, D, E
A, B, C, D, E, F, G, H
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

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
BA [auth G]
EA [auth H]
J [auth A]
M [auth B]
P [auth C]
BA [auth G],
EA [auth H],
J [auth A],
M [auth B],
P [auth C],
S [auth D],
V [auth E],
Y [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
CA [auth G]
FA [auth H]
K [auth A]
N [auth B]
Q [auth C]
CA [auth G],
FA [auth H],
K [auth A],
N [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG

Query on MG



Download:Ideal Coordinates CCD File
AA [auth G]
DA [auth H]
I [auth A]
L [auth B]
O [auth C]
AA [auth G],
DA [auth H],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.269 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 261.45α = 90
b = 161.92β = 124.12
c = 147.37γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-10-30
    Changes: Data collection, Refinement description, Structure summary