Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C7  (3D View)
Global Stoichiometry: Hetero 21-mer - A14B7 Pseudo Symmetry: Cyclic - C7  (3D View)
Pseudo Stoichiometry: Hetero 21-mer - A7B7C7 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 849.05 kDa 
• Atom Count: 59283 
• Modelled Residue Count: 8015 
• Deposited Residue Count: 8015 
• Unique protein chains: 2

1PF9

GroEL-GroES-ADP

• PDB DOI: 10.2210/pdb1PF9/pdb

• Classification: CHAPERONE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-05-24 Released: 2003-11-04 
• Deposition Author(s): Chaudhry, C., Farr, G.W., Todd, M.J., Rye, H.S., Brunger, A.T., Adams, P.D., Horwich, A.L., Sigler, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.287 
• R-Value Work: 0.269 

Literature

Role of the gamma-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics.

Chaudhry, C., Farr, G.W., Todd, M.J., Rye, H.S., Brunger, A.T., Adams, P.D., Horwich, A.L., Sigler, P.B.

(2003) EMBO J 22: 4877-4887

• PubMed: 14517228 
• DOI: 10.1093/emboj/cdg477
• Primary Citation of Related Structures:  
  1PCQ, 1PF9


• PubMed Abstract: 
  

Productive cis folding by the chaperonin GroEL is triggered by the binding of ATP but not ADP, along with cochaperonin GroES, to the same ring as non-native polypeptide, ejecting polypeptide into an encapsulated hydrophilic chamber. We examined the specific contribution of the gamma-phosphate of ATP to this activation process using complexes of ADP and aluminium or beryllium fluoride. These ATP analogues supported productive cis folding of the substrate protein, rhodanese, even when added to already-formed, folding-inactive cis ADP ternary complexes, essentially introducing the gamma-phosphate of ATP in an independent step. Aluminium fluoride was observed to stabilize the association of GroES with GroEL, with a substantial release of free energy (-46 kcal/mol). To understand the basis of such activation and stabilization, a crystal structure of GroEL-GroES-ADP.AlF3 was determined at 2.8 A. A trigonal AlF3 metal complex was observed in the gamma-phosphate position of the nucleotide pocket of the cis ring. Surprisingly, when this structure was compared with that of the previously determined GroEL-GroES-ADP complex, no other differences were observed. We discuss the likely basis of the ability of gamma-phosphate binding to convert preformed GroEL-GroES-ADP-polypeptide complexes into the folding-active state.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
groEL protein	A, B, C, D, E, F, G, H, I, J, K, L, M, N	524	Escherichia coli	Mutation(s): 0  Gene Names: GROL OR GROEL OR MOPA OR B4143 OR C5227 OR Z5748 OR ECS5124 OR SF4297 EC: 5.6.1.7
UniProt
Find proteins for P0A6F5 (Escherichia coli (strain K12)) Explore P0A6F5  Go to UniProtKB:  P0A6F5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
groES protein	O, P, Q, R, S, T, U	97	Escherichia coli	Mutation(s): 0  Gene Names: GROS OR GROES OR MOPB OR B4142 OR C5226 OR Z5747 OR ECS5123 OR SF4296
UniProt
Find proteins for P0A6F9 (Escherichia coli (strain K12)) Explore P0A6F9  Go to UniProtKB:  P0A6F9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	AA [auth C], CA [auth D], EA [auth E], GA [auth F], IA [auth G], W [auth A], Y [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	BA [auth D], DA [auth E], FA [auth F], HA [auth G], V [auth A], X [auth B], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.287 
• R-Value Work: 0.269 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 255.26	α = 90
b = 265.25	β = 90
c = 184.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-24 
• Released Date: 2003-11-04 
Deposition Author(s): Chaudhry, C., Farr, G.W., Todd, M.J., Rye, H.S., Brunger, A.T., Adams, P.D., Horwich, A.L., Sigler, P.B.

Revision History  

• Version 1.0: 2003-11-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance