3E76

Crystal structure of Wild-type GroEL with bound Thallium ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.262 

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Ligand Structure Quality Assessment 


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Literature

Use of thallium to identify monovalent cation binding sites in GroEL.

Kiser, P.D.Lorimer, G.H.Palczewski, K.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 967-971

  • DOI: 10.1107/S1744309109032928
  • Primary Citation of Related Structures:  
    3E76

  • PubMed Abstract: 
  • GroEL is a bacterial chaperone protein that assembles into a homotetradecameric complex exhibiting D(7) symmetry and utilizes the co-chaperone protein GroES and ATP hydrolysis to assist in the proper folding of a variety of cytosolic proteins. GroEL utilizes two metal cofactors, Mg(2+) and K(+), to bind and hydrolyze ATP ...

    GroEL is a bacterial chaperone protein that assembles into a homotetradecameric complex exhibiting D(7) symmetry and utilizes the co-chaperone protein GroES and ATP hydrolysis to assist in the proper folding of a variety of cytosolic proteins. GroEL utilizes two metal cofactors, Mg(2+) and K(+), to bind and hydrolyze ATP. A K(+)-binding site has been proposed to be located next to the nucleotide-binding site, but the available structural data do not firmly support this conclusion. Moreover, more than one functionally significant K(+)-binding site may exist within GroEL. Because K(+) has important and complex effects on GroEL activity and is involved in both positive (intra-ring) and negative (inter-ring) cooperativity for ATP hydrolysis, it is important to determine the exact location of these cation-binding site(s) within GroEL. In this study, the K(+) mimetic Tl(+) was incorporated into GroEL crystals, a moderately redundant 3.94 A resolution X-ray diffraction data set was collected from a single crystal and the strong anomalous scattering signal from the thallium ion was used to identify monovalent cation-binding sites. The results confirmed the previously proposed placement of K(+) next to the nucleotide-binding site and also identified additional binding sites that may be important for GroEL function and cooperativity. These findings also demonstrate the general usefulness of Tl(+) for the identification of monovalent cation-binding sites in protein crystal structures, even when the quality and resolution of the diffraction data are relatively low.


    Organizational Affiliation

    Case Western Reserve University, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
60 kDa chaperonin
A, B, C, D, E, F, G, H, I, J, K, L, M, N
A, B, C, D, E, F, G, H, I, J, K, L, M, N
547Escherichia coli UTI89Mutation(s): 0 
Gene Names: groLgroELUTI89_C4741
EC: 3.6.4.9 (PDB Primary Data), 5.6.1.7 (UniProt)
UniProt
Find proteins for Q1R3B6 (Escherichia coli (strain UTI89 / UPEC))
Explore Q1R3B6 
Go to UniProtKB:  Q1R3B6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1R3B6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
AA [auth C],
BB [auth H],
BC [auth M],
FA [auth D],
GC [auth N],
AA [auth C],
BB [auth H],
BC [auth M],
FA [auth D],
GC [auth N],
HB [auth I],
LA [auth E],
MB [auth J],
O [auth A],
QA [auth F],
RB [auth K],
U [auth B],
WA [auth G],
WB [auth L]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
TL
Query on TL

Download Ideal Coordinates CCD File 
BA [auth C],
CA [auth C],
CB [auth H],
CC [auth M],
DA [auth C],
BA [auth C],
CA [auth C],
CB [auth H],
CC [auth M],
DA [auth C],
DB [auth H],
DC [auth M],
EB [auth H],
EC [auth M],
GA [auth D],
GB [auth H],
HA [auth D],
HC [auth N],
IA [auth D],
IB [auth I],
IC [auth N],
JB [auth I],
KA [auth D],
KB [auth I],
MA [auth E],
NA [auth E],
NB [auth J],
OA [auth E],
OB [auth J],
P [auth A],
PB [auth J],
Q [auth A],
R [auth A],
RA [auth F],
SA [auth F],
SB [auth K],
T [auth A],
TA [auth F],
TB [auth K],
UB [auth K],
V [auth B],
VA [auth F],
W [auth B],
X [auth B],
XA [auth G],
XB [auth L],
YA [auth G],
YB [auth L],
Z [auth B],
ZA [auth G],
ZB [auth L]
THALLIUM (I) ION
Tl
ZLUSCZLCHQSJRU-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth G],
AC [auth L],
EA [auth C],
FB [auth H],
FC [auth M],
AB [auth G],
AC [auth L],
EA [auth C],
FB [auth H],
FC [auth M],
JA [auth D],
JC [auth N],
LB [auth I],
PA [auth E],
QB [auth J],
S [auth A],
UA [auth F],
VB [auth K],
Y [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.262 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.676α = 90
b = 260.954β = 90
c = 287.872γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance