5LSP

107_A07 Fab in complex with fragment of the Met receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Characterization and structural determination of a new anti-MET function-blocking antibody with binding epitope distinct from the ligand binding domain.

DiCara, D.M.Chirgadze, D.Y.Pope, A.R.Karatt-Vellatt, A.Winter, A.Slavny, P.van den Heuvel, J.Parthiban, K.Holland, J.Packman, L.C.Mavria, G.Hoffmann, J.Birchmeier, W.Gherardi, E.McCafferty, J.

(2017) Sci Rep 7: 9000-9000

  • DOI: 10.1038/s41598-017-09460-2
  • Primary Citation of Related Structures:  
    5LSP

  • PubMed Abstract: 
  • The growth and motility factor Hepatocyte Growth Factor/Scatter Factor (HGF/SF) and its receptor, the product of the MET proto-oncogene, promote invasion and metastasis of tumor cells and have been considered potential targets for cancer therapy. We ...

    The growth and motility factor Hepatocyte Growth Factor/Scatter Factor (HGF/SF) and its receptor, the product of the MET proto-oncogene, promote invasion and metastasis of tumor cells and have been considered potential targets for cancer therapy. We generated a new Met-blocking antibody which binds outside the ligand-binding site, and determined the crystal structure of the Fab in complex with its target, which identifies the binding site as the Met Ig1 domain. The antibody, 107_A07, inhibited HGF/SF-induced cell migration and proliferation in vitro and inhibited growth of tumor xenografts in vivo. In biochemical assays, 107_A07 competes with both HGF/SF and its truncated splice variant NK1 for MET binding, despite the location of the antibody epitope on a domain (Ig1) not reported to bind NK1 or HGF/SF. Overlay of the Fab-MET crystal structure with the InternalinB-MET crystal structure shows that the 107_A07 Fab comes into close proximity with the HGF/SF-binding SEMA domain when MET is in the "compact", InternalinB-bound conformation, but not when MET is in the "open" conformation. These findings provide further support for the importance of the "compact" conformation of the MET extracellular domain, and the relevance of this conformation to HGF/SF binding and signaling.


    Organizational Affiliation

    IONTAS Ltd, Babraham Institute, Babraham, Cambridgeshire, CB22 3AT, UK. jmc@iontas.co.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatocyte growth factor receptorAP231Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
107_A07 Fab heavy chainHS223Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
107_A07 Fab light chainLT216Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatocyte growth factor receptorXY14Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A, P
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.88α = 90
b = 82.279β = 90
c = 267.304γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.2: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary