7OCM | pdb_00007ocm

K1K1H6, a potent recombinant minimal hepatocyte growth factor/scatter factor mimic

• PDB DOI: https://doi.org/10.2210/pdb7OCM/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-04-27 Released: 2021-07-07 
• Deposition Author(s): de Jonge, H., de Nola, G., Gherardi, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Dimerization of kringle 1 domain from hepatocyte growth factor/scatter factor provides a potent MET receptor agonist.

de Nola, G., Leclercq, B., Mougel, A., Taront, S., Simonneau, C., Forneris, F., Adriaenssens, E., Drobecq, H., Iamele, L., Dubuquoy, L., Melnyk, O., Gherardi, E., de Jonge, H., Vicogne, J.

(2022) Life Sci Alliance 5

• PubMed: 35905995 
• DOI: https://doi.org/10.26508/lsa.202201424
• Primary Citation Related Structures: 
  7OCL, 7OCM


• PubMed Abstract: 
  

  Hepatocyte growth factor/scatter factor (HGF/SF) and its cognate receptor MET play several essential roles in embryogenesis and regeneration in postnatal life of epithelial organs such as the liver, kidney, lung, and pancreas, prompting a strong interest in harnessing HGF/SF-MET signalling for regeneration of epithelial organs after acute or chronic damage. The limited stability and tissue diffusion of native HGF/SF, however, which reflect the tightly controlled, local mechanism of action of the morphogen, have led to a major search of HGF/SF mimics for therapy. In this work, we describe the rational design, production, and characterization of K1K1, a novel minimal MET agonist consisting of two copies of the kringle 1 domain of HGF/SF in tandem orientation. K1K1 is highly stable and displays biological activities equivalent or superior to native HGF/SF in a variety of in vitro assay systems and in a mouse model of liver disease. These data suggest that this engineered ligand may find wide applications in acute and chronic diseases of the liver and other epithelial organs dependent of MET activation.

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Organizational Affiliation: 
• Department of Molecular Medicine, University of Pavia, Unit of Immunology and General Pathology Section, Pavia, Italy.
University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019, UMR 9017, CIIL, Center for Infection and Immunity of Lille, Lille, France.
University of Lille, Inserm, CHU Lille, U1286, INFINITE, Institute for Translational Research in Inflammation, Lille, France.
Roche Pharmaceutical Research and Early Development (pRED), Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland.
The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
University of Lille, CNRS, INSERM, CHU Lille, Centre Oscar Lambret, UMR 9020, UMR 1277, Canther, Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France.
Department of Molecular Medicine, University of Pavia, Unit of Immunology and General Pathology Section, Pavia, Italy [e-mail].
University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019, UMR 9017, CIIL, Center for Infection and Immunity of Lille, Lille, France [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 20.54 kDa 
• Atom Count: 1,559 
• Modeled Residue Count: 174 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor alpha chain,Hepatocyte growth factor alpha chain	A	176	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
EPE	B [auth A], C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.839	α = 90
b = 59.648	β = 103.85
c = 46.289	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
iMOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): de Jonge, H., de Nola, G., Gherardi, E.

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release
  
• Version 1.1: 2023-02-01
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary