Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A3B2C1D1E1 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - C2 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - D2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 149.68 kDa 
• Atom Count: 10159 
• Modelled Residue Count: 1319 
• Deposited Residue Count: 1368 
• Unique protein chains: 4

5LSP

107_A07 Fab in complex with fragment of the Met receptor

• PDB DOI: 10.2210/pdb5LSP/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Homo sapiens
• Mutation(s): No 


• Deposited: 2016-09-05 Released: 2017-09-13 
• Deposition Author(s): DiCara, D., Chirgadze, D.Y., Pope, A., Karatt-Vellatt, A., Winter, A., van den Heuvel, J., Gherardi, E., McCafferty, J.

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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 

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

• PubMed: 28827556 
• 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 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.

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Organizational Affiliation: 

IONTAS Ltd, Babraham Institute, Babraham, Cambridgeshire, CB22 3AT, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A, D [auth P]	231	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 GTEx:  ENSG00000105976

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
107_A07 Fab heavy chain	B [auth H], E [auth S]	223	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
107_A07 Fab light chain	C [auth L], F [auth T]	216	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	G [auth X], H [auth Y]	14	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 GTEx:  ENSG00000105976

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A], J [auth P]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 71.88	α = 90
b = 82.279	β = 90
c = 267.304	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-09-05 
• Released Date: 2017-09-13 
Deposition Author(s): DiCara, D., Chirgadze, D.Y., Pope, A., Karatt-Vellatt, A., Winter, A., van den Heuvel, J., Gherardi, E., McCafferty, J.

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