1XCK

Crystal structure of apo GroEL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of wild-type chaperonin GroEL

Bartolucci, C.Lamba, D.Grazulis, S.Manakova, E.Heumann, H.

(2005) J Mol Biol 354: 940-951

  • DOI: https://doi.org/10.1016/j.jmb.2005.09.096
  • Primary Citation of Related Structures:  
    1XCK

  • PubMed Abstract: 

    The 2.9A resolution crystal structure of apo wild-type GroEL was determined for the first time and represents the reference structure, facilitating the study of structural and functional differences observed in GroEL variants. Until now the crystal structure of the mutant Arg13Gly, Ala126Val GroEL was used for this purpose. We show that, due to the mutations as well as to the presence of a crystallographic symmetry, the ring-ring interface was inaccurately described. Analysis of the present structure allowed the definition of structural elements at this interface, essential for understanding the inter-ring allosteric signal transmission. We also show unambiguously that there is no ATP-induced 102 degrees rotation of the apical domain helix I around its helical axis, as previously assumed in the crystal structure of the (GroEL-KMgATP)(14) complex, and analyze the apical domain movements. These results enabled us to compare our structure with other GroEL crystal structures already published, allowing us to suggest a new route through which the allosteric signal for negative cooperativity propagates within the molecule. The proposed mechanism, supported by known mutagenesis data, underlines the importance of the switching of salt bridges.


  • Organizational Affiliation

    Istituto di Cristallografia, CNR, P.O. Box 10, I-00016 Monterotondo Stazione Roma, Italy. cecilia.bartolucci@ic.cnr.it


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60 kDa chaperonin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
547Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A6F5 (Escherichia coli (strain K12))
Explore P0A6F5 
Go to UniProtKB:  P0A6F5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6F5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
EB [auth F]
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
EB [auth F],
EC [auth J],
FB [auth F],
GB [auth F],
IC [auth K],
JC [auth K],
KA [auth C],
LB [auth G],
MB [auth G],
NC [auth L],
RA [auth D],
RB [auth H],
SB [auth H],
SC [auth M],
T [auth A],
U [auth A],
VA [auth E],
WA [auth E],
WB [auth I],
WC [auth N],
XA [auth E],
XB [auth I],
XC [auth N],
YA [auth E],
YB [auth I],
YC [auth N],
ZA [auth E]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AB [auth E]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AC [auth J]
BB [auth F]
BC [auth J]
CB [auth F]
CC [auth J]
AC [auth J],
BB [auth F],
BC [auth J],
CB [auth F],
CC [auth J],
FA [auth C],
FC [auth K],
GA [auth C],
GC [auth K],
HA [auth C],
HB [auth G],
IA [auth C],
IB [auth G],
JB [auth G],
KC [auth L],
LA [auth D],
LC [auth L],
MA [auth D],
NA [auth D],
NB [auth H],
O [auth A],
OA [auth D],
OB [auth H],
OC [auth M],
P [auth A],
PA [auth D],
PB [auth H],
PC [auth M],
Q [auth A],
QC [auth M],
R [auth A],
SA [auth E],
TA [auth E],
TB [auth I],
TC [auth N],
UB [auth I],
UC [auth N],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B],
ZB [auth J]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth B]
DB [auth F]
DC [auth J]
HC [auth K]
JA [auth C]
AA [auth B],
DB [auth F],
DC [auth J],
HC [auth K],
JA [auth C],
KB [auth G],
MC [auth L],
QA [auth D],
QB [auth H],
RC [auth M],
S [auth A],
UA [auth E],
VB [auth I],
VC [auth N]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 262.8α = 90
b = 283.6β = 90
c = 135.72γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description