3KO1 | pdb_00003ko1

Cystal structure of thermosome from Acidianus tengchongensis strain S5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 
    0.283 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.277 (Depositor) 
  • R-Value Observed: 
    0.277 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of group II chaperonin in the open state.

Huo, Y.Hu, Z.Zhang, K.Wang, L.Zhai, Y.Zhou, Q.Lander, G.Zhu, J.He, Y.Pang, X.Xu, W.Bartlam, M.Dong, Z.Sun, F.

(2010) Structure 18: 1270-1279

  • DOI: https://doi.org/10.1016/j.str.2010.07.009
  • Primary Citation Related Structures: 
    3KO1

  • PubMed Abstract: 

    Thermosomes are group II chaperonins responsible for protein refolding in an ATP-dependent manner. Little is known regarding the conformational changes of thermosomes during their functional cycle due to a lack of high-resolution structure in the open state. Here, we report the first complete crystal structure of thermosome (rATcpnβ) in the open state from Acidianus tengchongensis. There is a ∼30° rotation of the apical and lid domains compared with the previous closed structure. Besides, the structure reveals a conspicuous hydrophobic patch in the lid domain, and residues locating in this patch are conserved across species. Both the closed and open forms of rATcpnβ were also reconstructed by electron microscopy (EM). Structural fitting revealed the detailed conformational change from the open to the closed state. Structural comparison as well as protease K digestion indicated only ATP binding without hydrolysis does not induce chamber closure of thermosome.


  • Organizational Affiliation
    • National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecule Content 

  • Total Structure Weight: 541.49 kDa 
  • Atom Count: 34,884 
  • Modeled Residue Count: 4,545 
  • Deposited Residue Count: 4,977 
  • 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, I
553Acidianus tengchongensisMutation(s): 0 
UniProt
Find proteins for Q877H2 (Acidianus tengchongensis)
Explore Q877H2 
Go to UniProtKB:  Q877H2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ877H2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
J [auth A]
K [auth B]
L [auth C]
M [auth D]
N [auth E]
J [auth A],
K [auth B],
L [auth C],
M [auth D],
N [auth E],
O [auth F],
P [auth G],
Q [auth H],
R [auth I]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free:  0.283 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.277 (Depositor) 
  • R-Value Observed: 0.277 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.674α = 90
b = 283.042β = 133.9
c = 160.75γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
CNSrefinement
MOSFLMdata reduction
SCALAdata 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: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description