Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 42344.55 
• Atom Count: 2764 
• Residue Count: 366 
• Unique protein chains: 1

1NK1

NK1 FRAGMENT OF HUMAN HEPATOCYTE GROWTH FACTOR/SCATTER FACTOR (HGF/SF) AT 2.5 ANGSTROM RESOLUTION

• DOI: 10.2210/pdb1NK1/pdb

• Classification: HORMONE/GROWTH FACTOR
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): 1 


• Deposited: 1998-08-20 Released: 1999-01-13 
• Deposition Author(s): Chirgadze, D.Y., Hepple, J.P., Zhou, H., Byrd, R.A., Blundell, T.L., Gherardi, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.319 
• R-Value Work: 0.245 

Literature

Crystal structure of the NK1 fragment of HGF/SF suggests a novel mode for growth factor dimerization and receptor binding.

Chirgadze, D.Y., Hepple, J.P., Zhou, H., Byrd, R.A., Blundell, T.L., Gherardi, E.

(1999) Nat.Struct.Mol.Biol. 6: 72-79

• PubMed: 9886295 
• DOI: 10.1038/4947


• PubMed Abstract: 
  

Although ligand-induced receptor dimerization is a common prerequisite for receptor activation, the mode by which different growth factors bind their receptors and cause them to dimerize varies considerably. Here we report the crystal structure at 2.5 A resolution of NK1, a receptor-binding fragment and a natural splice variant of hepatocyte growth factor/scatter factor (HGF/SF). NK1 assembles as a homodimer in the asymmetric unit, revealing a novel mode of growth factor dimerization produced by close packing of the N domain of one subunit and the kringle domain of the other, thus bringing the two linkers in close proximity. The structure suggests the presence of a binding site for heparan sulfate chains and a mechanism by which the NK1 dimer may engage two receptor molecules through clusters of amino acids located on each protomer and on opposite surfaces of the homodimer. We also report that short (14-mer) heparin fragments effectively dimerize NK1 in solution, implying that heparan sulfate chains may stabilize the NK1 dimer. These results provide a basis for the agonistic activity of NK1 and have implications for the mechanism of receptor binding of HGF/SF.

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Organizational Affiliation: 

Department of Biochemistry, University of Cambridge, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (HEPATOCYTE GROWTH FACTOR PRECURSOR)	A, B	183	Homo sapiens	Mutation(s): 1  Gene Names: HGF (HPTA)
Find proteins for P14210 (Homo sapiens) Go to Gene View: HGF Go to UniProtKB:  P14210

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.319 
• R-Value Work: 0.245 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 53.420	α = 90.00
b = 63.560	β = 96.04
c = 56.810	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-08-20 
• Released Date: 1999-01-13 
• Deposition Author(s): Chirgadze, D.Y., Hepple, J.P., Zhou, H., Byrd, R.A., Blundell, T.L., Gherardi, E.

Revision History 

• Version 1.0: 1999-01-13
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance