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 


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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: 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cpn60(GroEL)
A,
B,
C,
D,
E,
543Thermus thermophilusMutation(s): 0 
EC: 5.6.1.7
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cpn10(GroES)
O,
P,
Q,
R,
S,
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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