Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 57.93 kDa 
• Atom Count: 3560 
• Modelled Residue Count: 432 
• Deposited Residue Count: 502 
• Unique protein chains: 1

4Z1F

Crystal structure of human Trap1 with PU-H71

• PDB DOI: 10.2210/pdb4Z1F/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-27 Released: 2015-04-22 
• Deposition Author(s): Lee, C., Park, H.K., Ryu, J.H., Kang, B.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.280 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 

Literature

Development of a Mitochondria-Targeted Hsp90 Inhibitor Based on the Crystal Structures of Human TRAP1

Lee, C., Park, H.K., Jeong, H., Lim, J., Lee, A.J., Cheon, K.Y., Kim, C.S., Thomas, A.P., Bae, B., Kim, N.D., Kim, S.H., Suh, P.G., Ryu, J.H., Kang, B.H.

(2015) J Am Chem Soc 137: 4358-4367

• PubMed: 25785725 
• DOI: 10.1021/ja511893n
• Primary Citation of Related Structures:  
  4Z1F, 4Z1G, 4Z1H, 4Z1I


• PubMed Abstract: 
  

The mitochondrial pool of Hsp90 and its mitochondrial paralogue, TRAP1, suppresses cell death and reprograms energy metabolism in cancer cells; therefore, Hsp90 and TRAP1 have been suggested as target proteins for anticancer drug development. Here, we report that the actual target protein in cancer cell mitochondria is TRAP1, and current Hsp90 inhibitors cannot effectively inactivate TRAP1 because of their insufficient accumulation in the mitochondria. To develop mitochondrial TRAP1 inhibitors, we determined the crystal structures of human TRAP1 complexed with Hsp90 inhibitors. The isopropyl amine of the Hsp90 inhibitor PU-H71 was replaced with the mitochondria-targeting moiety triphenylphosphonium to produce SMTIN-P01. SMTIN-P01 showed a different mode of action from the nontargeted PU-H71, as well as much improved cytotoxicity to cancer cells. In addition, we determined the structure of a TRAP1-adenylyl-imidodiphosphate (AMP-PNP) complex. On the basis of comparative analysis of TRAP1 structures, we propose a molecular mechanism of ATP hydrolysis that is crucial for chaperone function.

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Organizational Affiliation: 

∥New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 701-310, Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein 75 kDa, mitochondrial	A	502	Homo sapiens	Mutation(s): 0  Gene Names: TRAP1, HSP75
UniProt & NIH Common Fund Data Resources
Find proteins for Q12931 (Homo sapiens) Explore Q12931  Go to UniProtKB:  Q12931
PHAROS:  Q12931 GTEx:  ENSG00000126602

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H71	B [auth A]	8-[(6-IODO-1,3-BENZODIOXOL-5-YL)THIO]-9-[3-(ISOPROPYLAMINO)PROPYL]-9H-PURIN-6-AMINE C18 H21 I N6 O2 S SUPVGFZUWFMATN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
H71	BindingDB:  4Z1F	IC50: min: 205, max: 675 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.280 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.223	α = 90
b = 69.223	β = 90
c = 252.522	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-03-27 
• Released Date: 2015-04-22 
Deposition Author(s): Lee, C., Park, H.K., Ryu, J.H., Kang, B.H.

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release