Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 45.23 kDa 
• Atom Count: 3090 
• Modelled Residue Count: 356 
• Deposited Residue Count: 390 
• Unique protein chains: 2

1H2K

Factor Inhibiting HIF-1 alpha in complex with HIF-1 alpha fragment peptide

• PDB DOI: 10.2210/pdb1H2K/pdb

• Classification: TRANSCRIPTION ACTIVATOR/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-08-12 Released: 2002-11-28 
• Deposition Author(s): Elkins, J.M., Hewitson, K.S., McNeill, L.A., Schlemminger, I., Seibel, J.F., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.213 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Literature

Structure of Factor-Inhibiting Hypoxia-Inducible Factor (Hif) Reveals Mechanism of Oxidative Modification of Hif-1Alpha

Elkins, J.M., Hewitson, K.S., McNeill, L.A., Seibel, J.F., Schlemminger, I., Pugh, C., Ratcliffe, P., Schofield, C.J.

(2003) J Biol Chem 278: 1802-1806

• PubMed: 12446723 
• DOI: 10.1074/jbc.C200644200
• Primary Citation of Related Structures:  
  1H2K, 1H2L, 1H2M, 1H2N


• PubMed Abstract: 
  

The activity of the transcription factor hypoxia-inducible factor (HIF) is regulated by oxygen-dependent hydroxylation. Under normoxic conditions, hydroxylation of proline residues triggers destruction of its alpha-subunit while hydroxylation of Asn(803) in the C-terminal transactivation domain of HIF-1 alpha (CAD) prevents its interaction with p300. Here we report crystal structures of the asparagine hydroxylase (factor-inhibiting HIF, FIH) complexed with Fe((II)), 2-oxoglutarate cosubstrate, and CAD fragments, which reveal the structural basis of HIF modification. CAD binding to FIH occurs via an induced fit process at two distinct interaction sites. At the hydroxylation site CAD adopts a loop conformation, contrasting with a helical conformation for the same residues when bound to p300. Asn(803) of CAD is buried and precisely orientated in the active site such that hydroxylation occurs at its beta-carbon. Together with structures with the inhibitors Zn((II)) and N-oxaloylglycine, analysis of the FIH-CAD complexes will assist design of hydroxylase inhibitors with proangiogenic properties. Conserved structural motifs within FIH imply it is one of an extended family of Fe((II)) oxygenases involved in gene regulation.

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Organizational Affiliation: 

Oxford Centre for Molecular Sciences and the Dyson Perrins Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QY, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FACTOR INHIBITING HIF1	A	349	Homo sapiens	Mutation(s): 0  Gene Names: HIF1AN, FIH1 EC: 1.14.11.30 (UniProt), 1.14.11 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWT6 (Homo sapiens) Explore Q9NWT6  Go to UniProtKB:  Q9NWT6
PHAROS:  Q9NWT6 GTEx:  ENSG00000166135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOXIA-INDUCIBLE FACTOR 1 ALPHA	B [auth S]	41	Homo sapiens	Mutation(s): 0  Gene Names: 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OGA	D [auth A]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE2	C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OGA	BindingDB:  1H2K	Ki: 1.20e+6 (nM) from 1 assay(s)
	PDBBind:  1H2K	Ki: 1.20e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.213 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.161	α = 90
b = 86.161	β = 90
c = 146.656	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-08-12 
• Released Date: 2002-11-28 
Deposition Author(s): Elkins, J.M., Hewitson, K.S., McNeill, L.A., Schlemminger, I., Seibel, J.F., Schofield, C.J.

Revision History  

• Version 1.0: 2002-11-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-02-21
  Changes: Database references