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- PDB-1buv: CRYSTAL STRUCTURE OF THE MT1-MMP-TIMP-2 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1buv
TitleCRYSTAL STRUCTURE OF THE MT1-MMP-TIMP-2 COMPLEX
Components
  • PROTEIN (MEMBRANE-TYPE MATRIX METALLOPROTEINASE (CDMT1-MMP))
  • PROTEIN (METALLOPROTEINASE INHIBITOR (TIMP-2))
KeywordsHYDROLASE/HYDROLASE INHIBITOR / MATRIX METALLOPROTEINASE / TISSUE INHIBITOR OF METALLOPROTEINASES / PROTEINASE COMPLEX / PRO-GELATINASE A ACTIVATOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


membrane-type matrix metalloproteinase-1 / negative regulation of GDF15-GFRAL signaling pathway / positive regulation of macrophage migration / craniofacial suture morphogenesis / macropinosome / response to odorant / negative regulation of membrane protein ectodomain proteolysis / chondrocyte proliferation / head development / metalloendopeptidase inhibitor activity ...membrane-type matrix metalloproteinase-1 / negative regulation of GDF15-GFRAL signaling pathway / positive regulation of macrophage migration / craniofacial suture morphogenesis / macropinosome / response to odorant / negative regulation of membrane protein ectodomain proteolysis / chondrocyte proliferation / head development / metalloendopeptidase inhibitor activity / astrocyte cell migration / TGFBR3 PTM regulation / tissue remodeling / negative regulation of focal adhesion assembly / positive regulation of protein processing / endochondral ossification / embryonic cranial skeleton morphogenesis / intermediate filament cytoskeleton / endothelial cell proliferation / zymogen activation / positive regulation of B cell differentiation / branching morphogenesis of an epithelial tube / positive regulation of myotube differentiation / Activation of Matrix Metalloproteinases / metalloaminopeptidase activity / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / negative regulation of Notch signaling pathway / response to mechanical stimulus / regulation of protein localization to plasma membrane / ovarian follicle development / response to hormone / Degradation of the extracellular matrix / response to cytokine / extracellular matrix organization / extracellular matrix / lung development / skeletal system development / cell motility / protein catabolic process / metalloendopeptidase activity / protein processing / Golgi lumen / response to estrogen / male gonad development / integrin binding / melanosome / positive regulation of cell growth / response to oxidative stress / cytoplasmic vesicle / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / angiogenesis / endopeptidase activity / response to hypoxia / positive regulation of cell migration / serine-type endopeptidase activity / focal adhesion / proteolysis / extracellular space / zinc ion binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / 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. ...Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / 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) / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Metalloproteinase inhibitor 2 / Matrix metalloproteinase-14
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsFernandez-Catalan, C. / Bode, W. / Huber, R. / Turk, D. / Calvete, J.J. / Lichte, A. / Tschesche, H. / Maskos, K.
CitationJournal: EMBO J. / Year: 1998
Title: Crystal structure of the complex formed by the membrane type 1-matrix metalloproteinase with the tissue inhibitor of metalloproteinases-2, the soluble progelatinase A receptor.
Authors: Fernandez-Catalan, C. / Bode, W. / Huber, R. / Turk, D. / Calvete, J.J. / Lichte, A. / Tschesche, H. / Maskos, K.
History
DepositionSep 7, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 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
M: PROTEIN (MEMBRANE-TYPE MATRIX METALLOPROTEINASE (CDMT1-MMP))
T: PROTEIN (METALLOPROTEINASE INHIBITOR (TIMP-2))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5356
Polymers40,3242
Non-polymers2114
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-76 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.650, 40.100, 85.680
Angle α, β, γ (deg.)90.00, 102.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (MEMBRANE-TYPE MATRIX METALLOPROTEINASE (CDMT1-MMP))


Mass: 19795.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P50281, membrane-type matrix metalloproteinase-1
#2: Protein PROTEIN (METALLOPROTEINASE INHIBITOR (TIMP-2))


Mass: 20528.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P16368
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
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: 2.14 Å3/Da / Density % sol: 40 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mM1dropBaCl2
310 mM1dropMgCl2
45 mM1dropCaCl2
5100 mM1dropNaCl
6100 mMammonium sulfate1drop
716 %(w/v)PEG80001drop
8MES-NaOH1drop

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 11911 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.095
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.389 / % possible all: 93.2
Reflection
*PLUS
Num. measured all: 73215
Reflection shell
*PLUS
% possible obs: 93.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.248 --RANDOM
Rwork0.189 ---
obs0.189 11911 97 %-
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 4 0 2839
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.88
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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