4V4O

Crystal Structure of the Chaperonin Complex Cpn60/Cpn10/(ADP)7 from Thermus Thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the native chaperonin complex from Thermus thermophilus revealed unexpected asymmetry at the cis-cavity

Shimamura, T.Koike-Takeshita, A.Yokoyama, K.Masui, R.Murai, N.Yoshida, M.Taguchi, H.Iwata, S.

(2004) Structure 12: 1471-1480

  • DOI: https://doi.org/10.1016/j.str.2004.05.020
  • Primary Citation of Related Structures:  
    4V4O

  • PubMed Abstract: 

    The chaperonins GroEL and GroES are essential mediators of protein folding. GroEL binds nonnative protein, ATP, and GroES, generating a ternary complex in which protein folding occurs within the cavity capped by GroES (cis-cavity). We determined the crystal structure of the native GroEL-GroES-ADP homolog from Thermus thermophilus, with substrate proteins in the cis-cavity, at 2.8 A resolution. Twenty-four in vivo substrate proteins within the cis-cavity were identified from the crystals. The structure around the cis-cavity, which encapsulates substrate proteins, shows significant differences from that observed for the substrate-free Escherichia coli GroEL-GroES complex. The apical domain around the cis-cavity of the Thermus GroEL-GroES complex exhibits a large deviation from the 7-fold symmetry. As a result, the GroEL-GroES interface differs considerably from the previously reported E. coli GroEL-GroES complex, including a previously unknown contact between GroEL and GroES.


  • Organizational Affiliation

    Department of Biological Sciences, Imperial College London, London SW7 2AZ, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cpn60(GroEL)543Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P61490 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore P61490 
Go to UniProtKB:  P61490
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61490
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
cpn10(GroES)100Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P61492 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore P61492 
Go to UniProtKB:  P61492
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61492
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
BB [auth F]
DB [auth G]
MB [auth a]
OB [auth b]
QB [auth c]
BB [auth F],
DB [auth G],
MB [auth a],
OB [auth b],
QB [auth c],
RA [auth A],
SB [auth d],
TA [auth B],
UB [auth e],
VA [auth C],
WB [auth f],
XA [auth D],
YB [auth g],
ZA [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
AC [auth i]
BC [auth j]
CC [auth k]
DC [auth l]
EB [auth H]
AC [auth i],
BC [auth j],
CC [auth k],
DC [auth l],
EB [auth H],
EC [auth m],
FB [auth I],
FC [auth n],
GB [auth J],
HB [auth K],
IB [auth L],
JB [auth M],
KB [auth N],
ZB [auth h]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth F]
CB [auth G]
LB [auth a]
NB [auth b]
PB [auth c]
AB [auth F],
CB [auth G],
LB [auth a],
NB [auth b],
PB [auth c],
QA [auth A],
RB [auth d],
SA [auth B],
TB [auth e],
UA [auth C],
VB [auth f],
WA [auth D],
XB [auth g],
YA [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.378α = 82.88
b = 156.424β = 85.35
c = 273.153γ = 68.52
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata 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: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations