3T10 | pdb_00003t10

HSP90 N-terminal domain bound to ACP

• PDB DOI: https://doi.org/10.2210/pdb3T10/pdb

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


• Deposited: 2011-07-21 Released: 2012-01-25 
• Deposition Author(s): Li, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 
  0.172 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Structure insights into mechanisms of ATP hydrolysis and the activation of human heat-shock protein 90.

Li, J., Sun, L., Xu, C., Yu, F., Zhou, H., Zhao, Y., Zhang, J., Cai, J., Mao, C., Tang, L., Xu, Y., He, J.

(2012) Acta Biochim Biophys Sin (Shanghai) 44: 300-306

• PubMed: 22318716 
• DOI: https://doi.org/10.1093/abbs/gms001
• Primary Citation Related Structures: 
  3T0H, 3T0Z, 3T10


• PubMed Abstract: 
  

  The activation of molecular chaperone heat-shock protein 90 (Hsp90) is dependent on ATP binding and hydrolysis, which occurs in the N-terminal domains of protein. Here, we have determined three crystal structures of the N-terminal domain of human Hsp90 in native and in complex with ATP and ATP analog, providing a clear view of the catalytic mechanism of ATP hydrolysis by Hsp90. Additionally, the binding of ATP leads the N-terminal domains to be an intermediate state that could be used to partially explain why the isolated N-terminal domain of Hsp90 has very weak ATP hydrolytic activity.

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Organizational Affiliation: 
• Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 26.19 kDa 
• Atom Count: 1,960 
• Modeled Residue Count: 214 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	228	Homo sapiens	Mutation(s): 0  Gene Names: HSP90A, HSP90AA1, HSPC1, HSPCA EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens) Explore P07900  Go to UniProtKB:  P07900
PHAROS:  P07900 GTEx:  ENSG00000080824

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACP	B [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free:  0.172 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.17	α = 90
b = 44.972	β = 115.15
c = 53.854	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Li, J.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2012-11-28
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description