4P3C | pdb_00004p3c

MT1-MMP:Fab complex (Form I)

PDB DOI: https://doi.org/10.2210/pdb4P3C/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
Expression System: Escherichia coli, Escherichia coli BL21
Mutation(s): No

Deposited: 2014-03-06 Released: 2014-12-17
Deposition Author(s): Rozenberg, H., Udi, Y., Sagi, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.200 (Depositor), 0.201 (DCC)
R-Value Work:
0.152 (Depositor), 0.154 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 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

PubMed: 25482542 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 49.87 kDa
Atom Count: 3,992
Modeled Residue Count: 449
Deposited Residue Count: 449
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain Fab fragment of antibody LEM-2/15	A [auth H]	218	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain Fab fragment of antibody LEM-2/15	B [auth L]	218	Mus musculus	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix metalloproteinase-14	C [auth M]	13	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50281
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain E [auth H] MOL2 format, chain E [auth H] mmCIF format, chain E [auth H]	E [auth H]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain N [auth L] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain N [auth L] mmCIF format, chain F [auth H] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain N [auth L]	F [auth H] G [auth H] H I [auth H] J [auth H] F [auth H], G [auth H], H, I [auth H], J [auth H], N [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain N [auth L] Interactions & Density Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain N [auth L]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain O [auth L] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain O [auth L] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H] mmCIF format, chain O [auth L]	K [auth H], L [auth H], O [auth L]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth H] Focus chain L [auth H] Focus chain O [auth L] Interactions & Density Focus chain K [auth H] Focus chain L [auth H] Focus chain O [auth L]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth L] MOL2 format, chain M [auth L] mmCIF format, chain M [auth L]	M [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth L] Interactions & Density Focus chain M [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.200 (Depositor), 0.201 (DCC)
R-Value Work: 0.152 (Depositor), 0.154 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.314	α = 90
b = 80.975	β = 90
c = 95.568	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-12-17

Deposition Author(s):

Rozenberg, H.

Udi, Y.

Sagi, I.

Revision History (Full details and data files)

Version 1.0: 2014-12-17
Type: Initial release
Version 1.1: 2015-01-14
Changes: Database references
Version 1.2: 2015-01-21
Changes: Database references
Version 1.3: 2015-02-18
Changes: Refinement description
Version 1.4: 2017-09-27
Changes: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
Version 1.5: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.6: 2024-10-30
Changes: Structure summary