Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 91.65 kDa 
• Atom Count: 5804 
• Residue Count: 727 
• Unique protein chains: 3

4O3T

Zymogen HGF-beta/MET with Zymogen Activator Peptide ZAP.14

• DOI: 10.2210/pdb4O3T/pdb

• Classification: transferase/growth factor
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2013-12-18 Released: 2014-06-04 
• Deposition Author(s): Eigenbrot, C., Landgraf, K.E., Steffek, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.276 
• R-Value Work: 0.232 
• R-Value Observed: 0.233 

Literature

An allosteric switch for pro-HGF/Met signaling using zymogen activator peptides.

Landgraf, K.E., Steffek, M., Quan, C., Tom, J., Yu, C., Santell, L., Maun, H.R., Eigenbrot, C., Lazarus, R.A.

(2014) Nat Chem Biol 10: 567-573

• PubMed: 24859116 
• DOI: 10.1038/nchembio.1533
• Primary Citation of Related Structures:  
  4O3T, 4O3U


• PubMed Abstract: 
  

Stimulation of hepatocyte growth factor (HGF) signaling through the Met receptor is an attractive approach for promoting tissue repair and preventing fibrosis. Using structure-guided peptide phage display combined with an activity-based sorting strategy, we engineered allosteric activators of zymogen-like pro-HGF to bypass proteolytic activation and reversibly stimulate pro-HGF signaling through Met. Biochemical, structural and biological data showed that zymogen activator peptides (ZAPtides) potently and selectively bind the activation pocket within the serine protease-like β-chain of pro-HGF and display titratable activation of pro-HGF-dependent Met signaling, leading to cell survival and migration. To further demonstrate the versatility of our ZAPtide platform, we identified allosteric activators for pro-macrophage stimulating protein and a zymogen serine protease, Protein C, which also provides evidence for target selectivity. These studies reveal that ZAPtides use molecular mimicry of the trypsin-like N-terminal insertion mechanism and establish a new paradigm for selective pharmacological activation of plasminogen-related growth factors and zymogen serine proteases.

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Organizational Affiliation: 

Department of Early Discovery Biochemistry, Genentech, Inc., San Francisco, California, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor	A	240	Homo sapiens	Mutation(s): 2  Gene Names: HGF, HPTA
Find proteins for P14210 (Homo sapiens) Explore P14210  Go to UniProtKB:  P14210
NIH Common Fund Data Resources
PHAROS  P14210 GTEx  ENSG00000019991

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
Find proteins for P08581 (Homo sapiens) Explore P08581  Go to UniProtKB:  P08581
NIH Common Fund Data Resources
PHAROS  P08581 GTEx  ENSG00000105976

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ZAP.14	P	11	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	A	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.276 
• R-Value Work: 0.232 
• R-Value Observed: 0.233 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.789	α = 90
b = 121.467	β = 90
c = 137.657	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-18 
• Released Date: 2014-06-04 
Deposition Author(s): Eigenbrot, C., Landgraf, K.E., Steffek, M.

Revision History 

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2014-07-02
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary