ATP-Triggered Conformational Changes Delineate Substrate-Binding and -Folding Mechanics of the Groel Chaperonin.

Clare, D.K; Vasishtan, D; Stagg, S; Quispe, J; Farr, G.W; Topf, M; Horwich, A.L; Saibil, H.R.

Macromolecule Content

Unique protein chains: 1

4AAQ

ATP-triggered molecular mechanics of the chaperonin GroEL

DOI: 10.2210/pdb4aaq/pdb
EMDataBank: EMD-1998

Classification: CHAPERONE
Deposited: 2011-12-05 Released: 2012-12-12
Deposition author(s): Clare, D.K., Vasishtan, D., Stagg, S., Quispe, J., Farr, G.W., Topf, M., Horwich, A.L., Saibil, H.R.
Organism: Escherichia coli
Expression System: ESCHERICHIA COLI
Mutation(s): 1

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 8.0 Å
Aggregation State: Particle
Reconstruction Method: Single Particle

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: CHAPERONE

Total Structure Weight: 807253.06

Macromolecule Entities
Molecule	Chains	Length	Organism	Details
60 KDA CHAPERONIN	A, B, C..., D, E, F, G, H, I, J, K, L, M, NA, B, C, D, E, F, G, H, I, J, K, L, M, N	548	Escherichia coli	Mutation: D398A Details: ATPASE MUTANT, ATP BOUND IN ONE RING. CHAINS A-G ARE IN THE RS1 ATP BOUND CONFORMATION CHAINS H-N ARE IN THE APO CONFORMATION. Gene Name(s): groL groEL mopA b4143 JW4103
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: P0A6F5 UniProt Full Protein Feature View for P0A6F5 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P0A6F5/4AAQ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
ATP Query on ATP Download SDF File Download CCD File	A, B, C, D, E, F, G	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N	Poseview Image of ATP in 4AAQ Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
PO4 Query on PO4 Download SDF File Download CCD File	A, B, C, D, E, F, G	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K	Poseview Image of PO4 in 4AAQ Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
MG Query on MG Download SDF File Download CCD File	A, B, C, D, E, F, G	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N	Poseview Image of MG in 4AAQ Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 8.0 Å
Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

Deposited Date: 2011-12-05
Released Date: 2012-12-12
Deposition author(s): Clare, D.K., Vasishtan, D., Stagg, S., Quispe, J., Farr, G.W., Topf, M., Horwich, A.L., Saibil, H.R.

Revision History

Version 1_0: 2012-12-12
Type: Initial release
Version 1_1: 2017-04-19
Type: Other
Version 1_2: 2017-08-30
Type: Data collection, Refinement description

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