Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 88.55 kDa 
• Atom Count: 5735 
• Modelled Residue Count: 727 
• Deposited Residue Count: 785 
• Unique protein chains: 2

1SHY

The Crystal Structure of HGF beta-chain in Complex with the Sema Domain of the Met Receptor.

• PDB DOI: 10.2210/pdb1SHY/pdb

• Classification: GROWTH FACTOR/GROWTH FACTOR RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2004-02-26 Released: 2004-06-15 
• Deposition Author(s): Stamos, J., Wiesmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free: 0.270 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 

Literature

Crystal structure of the HGF beta-chain in complex with the Sema domain of the Met receptor.

Stamos, J., Lazarus, R.A., Yao, X., Kirchhofer, D., Wiesmann, C.

(2004) EMBO J 23: 2325-2335

• PubMed: 15167892 
• DOI: 10.1038/sj.emboj.7600243
• Primary Citation of Related Structures:  
  1SHY


• PubMed Abstract: 
  

The Met tyrosine kinase receptor and its ligand, hepatocyte growth factor (HGF), play important roles in normal development and in tumor growth and metastasis. HGF-dependent signaling requires proteolysis from an inactive single-chain precursor into an active alpha/beta-heterodimer. We show that the serine protease-like HGF beta-chain alone binds Met, and report its crystal structure in complex with the Sema and PSI domain of the Met receptor. The Met Sema domain folds into a seven-bladed beta-propeller, where the bottom face of blades 2 and 3 binds to the HGF beta-chain 'active site region'. Mutation of HGF residues in the area that constitutes the active site region in related serine proteases significantly impairs HGF beta binding to Met. Key binding loops in this interface undergo conformational rearrangements upon maturation and explain the necessity of proteolytic cleavage for proper HGF signaling. A crystallographic dimer interface between two HGF beta-chains brings two HGF beta:Met complexes together, suggesting a possible mechanism of Met receptor dimerization and activation by HGF.

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Related Citations: 

• Structural and functional basis of the serine protease-like HGF b-chain in Met binding and signaling
  Kirchhofer, D., Xiaoyi, Y., Peek, M., Eigenbrot, C., Lipari, M.T., Billeci, K.L., Maun, H.R., Moran, P., Santell, L., Lazarus, R.A.
  () To be published --: --

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Organizational Affiliation: 

Department of Protein Engineering, Genentech Inc., South San Francisco, CA 94080, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor	A	234	Homo sapiens	Mutation(s): 1  Gene Names: HGF, HPTA
UniProt & NIH Common Fund Data Resources
Find proteins for P14210 (Homo sapiens) Explore P14210  Go to UniProtKB:  P14210
PHAROS:  P14210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	B	551	Homo sapiens	Mutation(s): 0  Gene Names: MET EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08581 (Homo sapiens) Explore P08581  Go to UniProtKB:  P08581
PHAROS:  P08581

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free: 0.270 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.052	α = 90
b = 186.352	β = 90
c = 66.659	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-02-26 
• Released Date: 2004-06-15 
Deposition Author(s): Stamos, J., Wiesmann, C.

Revision History  

• Version 1.0: 2004-06-15
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references