4P3D

MT1-MMP:Fab complex (Form II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.949 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Inhibition mechanism of membrane metalloprotease by an exosite-swiveling conformational antibody.

Udi, Y.Grossman, M.Solomonov, I.Dym, O.Rozenberg, H.Moreno, V.Cuniasse, P.Dive, V.Arroyo, A.G.Sagi, I.

(2015) Structure 23: 104-115

  • DOI: 10.1016/j.str.2014.10.012
  • Primary Citation of Related Structures:  4OUU, 4P3C, 4QXU

  • PubMed Abstract: 
  • Membrane type 1 metalloprotease (MT1-MMP) is a┬ámembrane-anchored, zinc-dependent protease. MT1-MMP is an important mediator of cell migration and invasion, and overexpression of this enzyme has been correlated with the malignancy of various tumor typ ...

    Membrane type 1 metalloprotease (MT1-MMP) is a membrane-anchored, zinc-dependent protease. MT1-MMP is an important mediator of cell migration and invasion, and overexpression of this enzyme has been correlated with the malignancy of various tumor types. Therefore, modulators of MT1-MMP activity are proposed to possess therapeutic potential in numerous invasive diseases. Here we report the inhibition mode of MT1-MMP by LEM-2/15 antibody, which targets a surface epitope of MT1-MMP. Specifically, the crystal structures of Fab LEM-2/15 in complex with the MT1-MMP surface antigen suggest that conformational swiveling of the enzyme surface loop is required for effective binding and consequent inhibition of MT1-MMP activity on the cell membrane. This inhibition mechanism appears to be effective in controlling active MT1-MMP in endothelial cells and at the leading edge of migratory cancer cells.


    Organizational Affiliation

    Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heavy Chain Fab fragment of antibody LEM-2/15
A, H
218N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Light Chain Fab fragment of antibody LEM-2/15
B, L
218N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Matrix metalloproteinase-14
C, M
13Homo sapiensGene Names: MMP14
EC: 3.4.24.80
Find proteins for P50281 (Homo sapiens)
Go to Gene View: MMP14
Go to UniProtKB:  P50281
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A, H
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
B, H, M
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.949 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.898α = 90.00
b = 96.226β = 92.36
c = 81.521γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
DNAdata collection
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references
  • Version 1.2: 2015-01-21
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy