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: 11.89 kDa 
• Atom Count: 896 
• Modelled Residue Count: 91 
• Deposited Residue Count: 101 
• Unique protein chains: 1

3HMS

Crystal Crystal structure of the N-terminal fragment (28-126) of the human hepatocyte growth factor/scatter factor, orthorhombic crystal form

• PDB DOI: 10.2210/pdb3HMS/pdb

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


• Deposited: 2009-05-29 Released: 2010-06-09 
• Deposition Author(s): Tolbert, W.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.255 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 

Literature

Structural basis for agonism and antagonism of hepatocyte growth factor.

Tolbert, W.D., Daugherty-Holtrop, J., Gherardi, E., Vande Woude, G., Xu, H.E.

(2010) Proc Natl Acad Sci U S A 107: 13264-13269

• PubMed: 20624990 
• DOI: 10.1073/pnas.1005183107
• Primary Citation of Related Structures:  
  3HMR, 3HMS, 3HMT, 3HN4


• PubMed Abstract: 
  

Hepatocyte growth factor (HGF) is an activating ligand of the Met receptor tyrosine kinase, whose activity is essential for normal tissue development and organ regeneration but abnormal activation of Met has been implicated in growth, invasion, and metastasis of many types of solid tumors. HGF has two natural splice variants, NK1 and NK2, which contain the N-terminal domain (N) and the first kringle (K1) or the first two kringle domains of HGF. NK1, which is a Met agonist, forms a head-to-tail dimer complex in crystal structures and mutations in the NK1 dimer interface convert NK1 to a Met antagonist. In contrast, NK2 is a Met antagonist, capable of inhibiting HGF's activity in cell proliferation without clear mechanism. Here we report the crystal structure of NK2, which forms a "closed" monomeric conformation through interdomain interactions between the N- domain and the second kringle domain (K2). Mutations that were designed to open up the NK2 closed conformation by disrupting the N/K2 interface convert NK2 from a Met antagonist to an agonist. Remarkably, this mutated NK2 agonist can be converted back to an antagonist by a mutation that disrupts the NK1/NK1 dimer interface. These results reveal the molecular determinants that regulate the agonist/antagonist properties of HGF NK2 and provide critical insights into the dimerization mechanism that regulates the Met receptor activation by HGF.

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Organizational Affiliation: 

Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Avenue, Grand Rapids, MI 49503, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor	A	101	Homo sapiens	Mutation(s): 0  Gene Names: HGF, HPTA
UniProt & NIH Common Fund Data Resources
Find proteins for P14210 (Homo sapiens) Explore P14210  Go to UniProtKB:  P14210
PHAROS:  P14210 GTEx:  ENSG00000019991

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.255 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.91	α = 90
b = 42.21	β = 90
c = 52.35	γ = 90

Software Package:

Software Name	Purpose
COM-CAT	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-29 
• Released Date: 2010-06-09 
Deposition Author(s): Tolbert, W.D.

Revision History  

• Version 1.0: 2010-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance