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- PDB-3ma2: Complex membrane type-1 matrix metalloproteinase (MT1-MMP) with t... -

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Basic information

Entry
Database: PDB / ID: 3ma2
TitleComplex membrane type-1 matrix metalloproteinase (MT1-MMP) with tissue inhibitor of metalloproteinase-1 (TIMP-1)
Components
  • Matrix metalloproteinase-14
  • Metalloproteinase inhibitor 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protein - protein complex / Cleavage on pair of basic residues / Disulfide bond / Membrane / Metal-binding / Metalloprotease / Protease / Transmembrane / Zymogen / Erythrocyte maturation / Glycoprotein / Metalloenzyme inhibitor / Metalloprotease inhibitor / Secreted / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


membrane-type matrix metalloproteinase-1 / negative regulation of GDF15-GFRAL signaling pathway / regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / craniofacial suture morphogenesis / positive regulation of macrophage migration / macropinosome / response to odorant / negative regulation of trophoblast cell migration / negative regulation of membrane protein ectodomain proteolysis ...membrane-type matrix metalloproteinase-1 / negative regulation of GDF15-GFRAL signaling pathway / regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / craniofacial suture morphogenesis / positive regulation of macrophage migration / macropinosome / response to odorant / negative regulation of trophoblast cell migration / negative regulation of membrane protein ectodomain proteolysis / chondrocyte proliferation / head development / connective tissue replacement involved in inflammatory response wound healing / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / astrocyte cell migration / tissue remodeling / negative regulation of catalytic activity / cellular response to UV-A / cellular response to peptide / negative regulation of endopeptidase activity / peptidase inhibitor activity / negative regulation of focal adhesion assembly / positive regulation of protein processing / endochondral ossification / intermediate filament cytoskeleton / embryonic cranial skeleton morphogenesis / endothelial cell proliferation / zymogen activation / cartilage development / positive regulation of B cell differentiation / branching morphogenesis of an epithelial tube / positive regulation of myotube differentiation / Interleukin-10 signaling / Activation of Matrix Metalloproteinases / endodermal cell differentiation / metalloaminopeptidase activity / Collagen degradation / collagen catabolic process / basement membrane / extracellular matrix disassembly / negative regulation of Notch signaling pathway / regulation of protein localization to plasma membrane / response to mechanical stimulus / ovarian follicle development / response to hormone / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / response to cytokine / platelet alpha granule lumen / cytokine activity / skeletal system development / Post-translational protein phosphorylation / cell motility / growth factor activity / lung development / protein catabolic process / : / protein processing / metalloendopeptidase activity / response to peptide hormone / Golgi lumen / response to estrogen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / male gonad development / integrin binding / melanosome / Platelet degranulation / protease binding / positive regulation of cell growth / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / cytoplasmic vesicle / Interleukin-4 and Interleukin-13 signaling / angiogenesis / endopeptidase activity / response to oxidative stress / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / serine-type endopeptidase activity / focal adhesion / positive regulation of cell population proliferation / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / Protease inhibitor I35 (TIMP) / Proteinase inhibitor I35b (TIMP), C-terminal / Tissue inhibitor of metalloproteinase, conserved site / Tissue inhibitor of metalloproteinase / Tissue inhibitors of metalloproteinases signature. / Tissue inhibitor of metalloproteinase family. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / PGBD superfamily ...Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / Protease inhibitor I35 (TIMP) / Proteinase inhibitor I35b (TIMP), C-terminal / Tissue inhibitor of metalloproteinase, conserved site / Tissue inhibitor of metalloproteinase / Tissue inhibitors of metalloproteinases signature. / Tissue inhibitor of metalloproteinase family. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / PGBD superfamily / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Metalloproteinase inhibitor 1 / Matrix metalloproteinase-14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGrossman, M. / Tworowski, D. / Dym, O. / Lee, M.-H. / Levy, Y. / Sagi, I.
CitationJournal: Biochemistry / Year: 2010
Title: The Intrinsic Protein Flexibility of Endogenous Protease Inhibitor TIMP-1 Controls Its Binding Interface and Affects Its Function.
Authors: Grossman, M. / Tworowski, D. / Dym, O. / Lee, M.H. / Levy, Y. / Murphy, G. / Sagi, I.
History
DepositionMar 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 28, 2015Group: Structure summary
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Matrix metalloproteinase-14
A: Matrix metalloproteinase-14
B: Metalloproteinase inhibitor 1
C: Metalloproteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,79812
Polymers69,3764
Non-polymers4228
Water2,612145
1
D: Matrix metalloproteinase-14
C: Metalloproteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8996
Polymers34,6882
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-12 kcal/mol
Surface area14000 Å2
MethodPISA
2
A: Matrix metalloproteinase-14
B: Metalloproteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8996
Polymers34,6882
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-13 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.690, 63.649, 87.158
Angle α, β, γ (deg.)90.00, 105.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Matrix metalloproteinase-14 / MMP-14 / Membrane-type matrix metalloproteinase 1 / MT-MMP 1 / MTMMP1 / Membrane-type-1 matrix ...MMP-14 / Membrane-type matrix metalloproteinase 1 / MT-MMP 1 / MTMMP1 / Membrane-type-1 matrix metalloproteinase / MT1-MMP / MT1MMP / MMP-X1


Mass: 20561.676 Da / Num. of mol.: 2 / Fragment: Residues 112-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP14 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P50281, membrane-type matrix metalloproteinase-1
#2: Protein Metalloproteinase inhibitor 1 / Tissue inhibitor of metalloproteinases 1 / TIMP-1 / Erythroid-potentiating activity / EPA / ...Tissue inhibitor of metalloproteinases 1 / TIMP-1 / Erythroid-potentiating activity / EPA / Fibroblast collagenase inhibitor / Collagenase inhibitor


Mass: 14126.209 Da / Num. of mol.: 2 / Fragment: Residues 24-148 / Mutation: V27A,P29V,T121L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMP1, CLGI, TIMP / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01033
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Bis-Tris pH 5.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 28, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 39106 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 24.36 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.103 / Net I/σ(I): 19.5
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1787 / Rsym value: 0.237 / % possible all: 90.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BQQ

1bqq


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.507 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24707 1961 5 %RANDOM
Rwork0.19644 ---
obs0.19905 37132 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.357 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å2-1.05 Å2
2---0.88 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4556 0 8 145 4709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0224695
X-RAY DIFFRACTIONr_angle_refined_deg2.4111.9236379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8335568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15723.404235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8915692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2491526
X-RAY DIFFRACTIONr_chiral_restr0.2480.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213702
X-RAY DIFFRACTIONr_mcbond_it1.4931.52852
X-RAY DIFFRACTIONr_mcangle_it2.43924571
X-RAY DIFFRACTIONr_scbond_it3.78231843
X-RAY DIFFRACTIONr_scangle_it5.4544.51808
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 111 -
Rwork0.243 2420 -
obs--87.01 %

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