Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 26.69 kDa 
• Atom Count: 1937 
• Modelled Residue Count: 217 
• Deposited Residue Count: 229 
• Unique protein chains: 2

4H6J

Identification of Cys 255 in HIF-1 as a novel site for development of covalent inhibitors of HIF-1 /ARNT PasB domain protein-protein interaction.

• DOI: 10.2210/pdb4H6J/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2012-09-19 Released: 2012-12-05 
• Deposition Author(s): Cardoso, R., Love, R.A., Nilsson, C., Bergqvist, S., Nowlin, D., Yan, J., Liu, K., Zhu, J., Chen, P., Deng, Y.-L., Dyson, H.J., Greig, M.J., Brooun, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.248 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 

Literature

Identification of Cys255 in HIF-1 alpha as a novel site for development of covalent inhibitors of HIF-1 alpha /ARNT PasB domain protein-protein interaction.

Cardoso, R., Love, R., Nilsson, C.L., Bergqvist, S., Nowlin, D., Yan, J., Liu, K.K., Zhu, J., Chen, P., Deng, Y.L., Dyson, H.J., Greig, M.J., Brooun, A.

(2012) Protein Sci 21: 1885-1896

• PubMed: 23033253 
• DOI: 10.1002/pro.2172
• Primary Citation of Related Structures:  
  4H6J


• PubMed Abstract: 
  

The heterodimer HIF-1α (hypoxia inducible factor)/HIF-β (also known as ARNT-aryl hydrocarbon nuclear translocator) is a key mediator of cellular response to hypoxia. The interaction between these monomer units can be modified by the action of small molecules in the binding interface between their C-terminal heterodimerization (PasB) domains. Taking advantage of the presence of several cysteine residues located in the allosteric cavity of HIF-1α PasB domain, we applied a cysteine-based reactomics "hotspot identification" strategy to locate regions of HIF-1α PasB domain critical for its interaction with ARNT. COMPOUND 5 was identified using a mass spectrometry-based primary screening strategy and was shown to react specifically with Cys255 of the HIF-1α PasB domain. Biophysical characterization of the interaction between PasB domains of HIF-1α and ARNT revealed that covalent binding of COMPOUND 5 to Cys255 reduced binding affinity between HIF-1α and ARNT PasB domains approximately 10-fold. Detailed NMR structural analysis of HIF-1α-PasB-COMPOUND 5 conjugate showed significant local conformation changes in the HIF-1α associated with key residues involved in the HIF-1α/ARNT PasB domain interaction as revealed by the crystal structure of the HIF-1α/ARNT PasB heterodimer. Our screening strategy could be applied to other targets to identify pockets surrounding reactive cysteines suitable for development of small molecule modulators of protein function.

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Organizational Affiliation: 

Oncology Chemistry, Worldwide Research and Development, Pfizer Inc., San Diego, California 92121, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOXIA INDUCIBLE FACTOR 1-ALPHA	A	113	Homo sapiens	Mutation(s): 1  Gene Names: HIF-1 alpha, HIF1A, BHLHE78, MOP1, PASD8
UniProt & NIH Common Fund Data Resources
Find proteins for Q16665 (Homo sapiens) Explore Q16665  Go to UniProtKB:  Q16665
PHAROS:  Q16665 GTEx:  ENSG00000100644

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARYL HYDROCARBON NUCLEAR TRANSLOCATOR	B	116	Homo sapiens	Mutation(s): 1  Gene Names: ARNT, BHLHE2
UniProt & NIH Common Fund Data Resources
Find proteins for P27540 (Homo sapiens) Explore P27540  Go to UniProtKB:  P27540
PHAROS:  P27540 GTEx:  ENSG00000143437

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.248 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.841	α = 90
b = 44.94	β = 96.54
c = 78.087	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CNX	refinement
PROCESS	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-09-19 
• Released Date: 2012-12-05 
Deposition Author(s): Cardoso, R., Love, R.A., Nilsson, C., Bergqvist, S., Nowlin, D., Yan, J., Liu, K., Zhu, J., Chen, P., Deng, Y.-L., Dyson, H.J., Greig, M.J., Brooun, A.

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2013-08-28
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Structure summary