4QXU | pdb_00004qxu

Novel Inhibition Mechanism of Membrane Metalloprotease by an Exosite-Swiveling Conformational antibody

• PDB DOI: https://doi.org/10.2210/pdb4QXU/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-22 Released: 2014-12-17 
• Deposition Author(s): Udi, Y., Grossman, M., Solomonov, I., Dym, O., Rozenberg, H., Moreno, v., Cuiniasse, P., Dive, V., Arroyo, A.G., Sagi, I., Israel Structural Proteomics Center (ISPC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.293 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

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

• PubMed: 25482542 
• DOI: https://doi.org/10.1016/j.str.2014.10.012
• Primary Citation Related Structures: 
  4OUU, 4P3C, 4P3D, 4QXU


• PubMed Abstract: 
  

  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.

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Organizational Affiliation: 
• Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel.
Structural Proteomics Unit and Department of Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel.
Vascular Biology and Inflammation Department, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, Madrid 28029, Spain.
Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Service d'Ingénierie Moléculaire de Protéines, Gif/Yvette 91191, France.
Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 50.64 kDa 
• Atom Count: 3,458 
• Modeled Residue Count: 450 
• Deposited Residue Count: 461 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti_MT1-MMP Light chain	A [auth L]	219	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti_MT1-MMP Heavy chain	B [auth H]	231	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix metalloproteinase-14	C [auth K]	11	Homo sapiens	Mutation(s): 0  Gene Names: MMP14 EC: 3.4.24.80
UniProt & NIH Common Fund Data Resources
Find proteins for P50281 (Homo sapiens) Explore P50281  Go to UniProtKB:  P50281
PHAROS:  P50281 GTEx:  ENSG00000157227

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth H], E [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.293 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.56	α = 90
b = 79.56	β = 90
c = 93.6	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-17 
Deposition Author(s): Udi, Y., Grossman, M., Solomonov, I., Dym, O., Rozenberg, H., Moreno, v., Cuiniasse, P., Dive, V., Arroyo, A.G., Sagi, I., Israel Structural Proteomics Center (ISPC)

Revision History  

• Version 1.0: 2014-12-17
  Type: Initial release
  
• Version 1.1: 2014-12-31
  Changes: Database references
• Version 1.2: 2015-01-28
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary