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- PDB-1uea: MMP-3/TIMP-1 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1uea
TitleMMP-3/TIMP-1 COMPLEX
Components
  • MATRIX METALLOPROTEINASE-3
  • TISSUE INHIBITOR OF METALLOPROTEINASE-1
KeywordsCOMPLEX (METALLOPROTEASE/INHIBITOR) / PROTEINASE / ZINC-ENDOPEPTIDASE / PROTEINASE INHIBITOR / COMPLEX / MMPS (MATRIX METALLO PROTEINASES) TIMPS (TISSUE INHIBITOR OF METALLO PROTEINASES) / METZINCINS / COMPLEX (METALLOPROTEASE-INHIBITOR) / COMPLEX (METALLOPROTEASE-INHIBITOR) complex
Function / homology
Function and homology information


regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / stromelysin 1 / peptidase inhibitor activity / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / negative regulation of membrane protein ectodomain proteolysis / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / cellular response to UV-A ...regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / stromelysin 1 / peptidase inhibitor activity / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / negative regulation of membrane protein ectodomain proteolysis / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / cellular response to UV-A / negative regulation of catalytic activity / regulation of neuroinflammatory response / negative regulation of endopeptidase activity / cartilage development / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / Interleukin-10 signaling / response to amyloid-beta / Collagen degradation / collagen catabolic process / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / extracellular matrix disassembly / cellular response to nitric oxide / negative regulation of reactive oxygen species metabolic process / EGFR Transactivation by Gastrin / Degradation of the extracellular matrix / regulation of cell migration / response to hormone / extracellular matrix organization / extracellular matrix / response to cytokine / platelet alpha granule lumen / cytokine activity / Post-translational protein phosphorylation / cellular response to amino acid stimulus / growth factor activity / positive regulation of protein-containing complex assembly / protein catabolic process / metalloendopeptidase activity / response to peptide hormone / cellular response to reactive oxygen species / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / metallopeptidase activity / Platelet degranulation / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / protease binding / endopeptidase activity / Extra-nuclear estrogen signaling / endoplasmic reticulum lumen / innate immune response / serine-type endopeptidase activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / mitochondrion / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleus / cytosol
Similarity search - Function
Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / 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 / Netrin domain ...Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / 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 / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / 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 1 / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsBode, W. / Maskos, K. / Gomis-Rueth, F.-X. / Nagase, H.
Citation
Journal: Nature / Year: 1997
Title: Mechanism of inhibition of the human matrix metalloproteinase stromelysin-1 by TIMP-1.
Authors: Gomis-Ruth, F.X. / Maskos, K. / Betz, M. / Bergner, A. / Huber, R. / Suzuki, K. / Yoshida, N. / Nagase, H. / Brew, K. / Bourenkov, G.P. / Bartunik, H. / Bode, W.
#1: Journal: FEBS Lett. / Year: 1996
Title: Folding and Characterization of the Amino-Terminal Domain of Human Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Expressed at High Yield in E. Coli
Authors: Huang, W. / Suzuki, K. / Nagase, H. / Arumugam, S. / Van Doren, S.R. / Brew, K.
#2: Journal: Protein Sci. / Year: 1995
Title: Stromelysin-1: Three-Dimensional Structure of the Inhibited Catalytic Domain and of the C-Truncated Proenzyme
Authors: Becker, J.W. / Marcy, A.I. / Rokosz, L.L. / Axel, M.G. / Burbaum, J.J. / Fitzgerald, P.M. / Cameron, P.M. / Esser, C.K. / Hagmann, W.K. / Hermes, J.D. / Springer, J.P.
History
DepositionJun 6, 1997Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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_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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
A: MATRIX METALLOPROTEINASE-3
B: TISSUE INHIBITOR OF METALLOPROTEINASE-1
C: MATRIX METALLOPROTEINASE-3
D: TISSUE INHIBITOR OF METALLOPROTEINASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,81614
Polymers80,3144
Non-polymers50210
Water9,206511
1
A: MATRIX METALLOPROTEINASE-3
B: TISSUE INHIBITOR OF METALLOPROTEINASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4087
Polymers40,1572
Non-polymers2515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-85 kcal/mol
Surface area16530 Å2
MethodPISA
2
C: MATRIX METALLOPROTEINASE-3
D: TISSUE INHIBITOR OF METALLOPROTEINASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4087
Polymers40,1572
Non-polymers2515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-83 kcal/mol
Surface area16770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.620, 80.620, 157.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsTHE ASYMMETRIC UNIT CONTAINS 2 MMP-3-TIMP-1 COMPLEXES, WITH MMP-3 (COMPLEX 1) RUNNING FROM A PHE 83 - A THR 255, WITH MET A 143 AND MET A 219 REPLACED BY SELENO-METHIONINE. 1ST CALCIUM: ATOM CA OF RESIDUE CA A 3. 2ND CALCIUM: ATOM CA OF RESIDUE CA A 4. 3RD CALCIUM: ATOM CA OF RESIDUE CA A 5. 1ST "STRUCTURAL" ZINC: ATOM ZN OF RESIDUE ZN A 1 2ND "CATALYTIC" ZINC: ATOM ZN OF RESIDUE ZN A 2 AND MMP-3 (COMPLEX 2) RUNNING FROM PHE C 83 - THR C 255, WITH MET C 143, AND MET C 219 REPLACED BY SELENO-METHIONINE. 1ST CALCIUM: ATOM CA OF RESIDUE CA C 3. 2ND CALCIUM: ATOM CA OF RESIDUE CA C 4. 3RD CALCIUM: ATOM CA OF RESIDUE CA C 5. 1ST "STRUCTURAL" ZINC: ATOM ZN OF RESIDUE ZN C 1 2ND "CATALYTIC" ZINC: ATOM ZN OF RESIDUE ZN C 2 AND TIMP-1 (COMPLEX 1) RUNNING FROM CYS B 1 - ALA B 184, WITH RESIDUES ASN B 30 AND ASN B 77 REPLACED BY ALA, AND (COMPLEX 2) RUNNING FROM CYS D 1 - ALA D 184, WITH RESIDUES ASN D 30 AND ASN D 77 REPLACED BY ALA. DISORDERED REGIONS LEFT OUT ARE A 251 - A 255, C 251 - C 255 (MMP-3), B 182 - B 184, D 182 - D 184 (TIMP-1); DISORDERED REGIONS ARBITRARILY MODELED AND CONTAINED IN THE COORDINATES ARE FROM C 226 - C 229 (MMP-3) AND B 55 - 56, B 153 - B 154, D 53 - D 55 (TIMP-1).

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Components

#1: Protein MATRIX METALLOPROTEINASE-3 / MMP-3 IS IDENTICAL WITH STROMELYSIN 1


Mass: 19510.318 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: SUBSTITUTION OF MET BY SELENOMET / Plasmid: PET3A-PROMMP-3(DC) / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P08254, stromelysin 1
#2: Protein TISSUE INHIBITOR OF METALLOPROTEINASE-1 / TIMP-1


Mass: 20646.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TIMPS ARE PROTEIN INHIBITORS OF MMPS / Source: (gene. exp.) Homo sapiens (human) / Description: UNGLYCOSYLATED / Plasmid: PEE14-TIMP-1 / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): CHO / References: UniProt: P01033
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 61 %
Description: WAVELENGTHS USED WERE F'' OF ZINC EDGE, CA. 1.279 ANGSTROMS, AND F'' OF SELENIUM EDGE, CA. 0.979 ANGSTROMS
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 M1reservoirNaCl
2200 mMepsilon-aminocaproic acid1reservoir
320 mMTris-HCl1reservoir
44 mM1reservoirCaCl2
5100 mMsodium acetate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.979, 1.279
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.2791
ReflectionResolution: 2.79→29.75 Å / Num. obs: 24252 / % possible obs: 99.6 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.11

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOSFLM/CCP4data collection
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data reduction
X-PLORphasing
RefinementResolution: 2.8→100 Å
Details: NUMBER OF PROTEIN ATOMS USED IN REFINEMENT: 5416 ACTIVE AND 106 PASSIVE NON-HYDROGEN ATOMS NUMBER OF HETEROGEN ATOMS: 2 X 2 ZN, 2 X 3 CA
RfactorNum. reflection
Rwork0.197 -
obs0.197 24138
Displacement parametersBiso mean: 41.4 Å2
Refinement stepCycle: LAST / Resolution: 2.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5522 0 10 510 6042
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.6
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 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.297
Solvent computation
*PLUS
Displacement parameters
*PLUS

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