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- PDB-1oo9: Orientation in Solution of MMP-3 Catalytic Domain and N-TIMP-1 fr... -

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Basic information

Entry
Database: PDB / ID: 1oo9
TitleOrientation in Solution of MMP-3 Catalytic Domain and N-TIMP-1 from Residual Dipolar Couplings
Components
  • Metalloproteinase inhibitor 1
  • Stromelysin-1
KeywordsHYDROLASE / PROTEIN-PROTEIN COMPLEX
Function / homology
Function and homology information


regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / stromelysin 1 / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / negative regulation of membrane protein ectodomain proteolysis / peptidase inhibitor activity / metalloendopeptidase inhibitor activity / cellular response to UV-A / negative regulation of catalytic activity ...regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / stromelysin 1 / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / negative regulation of membrane protein ectodomain proteolysis / peptidase inhibitor activity / metalloendopeptidase inhibitor activity / 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 / basement membrane / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide / negative regulation of reactive oxygen species metabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell migration / EGFR Transactivation by Gastrin / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / platelet alpha granule lumen / response to hormone / response to cytokine / cytokine activity / cellular response to amino acid stimulus / Post-translational protein phosphorylation / growth factor activity / protein catabolic process / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / response to peptide hormone / cellular response to reactive oxygen species / metallopeptidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / protease binding / Extra-nuclear estrogen signaling / endoplasmic reticulum lumen / serine-type endopeptidase activity / innate immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleus / cytosol
Similarity search - Function
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 ...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) / 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)
MethodSOLUTION NMR / RIGID BODY MINIMIZATION, RESTRAINED SIMULATED ANNEALING
AuthorsArumugam, S. / Van Doren, S.R.
CitationJournal: Biochemistry / Year: 2003
Title: Global Orientation of Bound MMP-3 and N-TIMP-1 in Solution via Residual Dipolar Couplings
Authors: Arumugam, S. / Van Doren, S.R.
History
DepositionMar 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stromelysin-1
B: Metalloproteinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)33,1562
Polymers33,1562
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 25lowest energy structure
Representative

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Components

#1: Protein Stromelysin-1 / Matrix metalloproteinase-3 / MMP-3 / Transin-1 / SL-1


Mass: 18887.029 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP3 OR STMY1 / Plasmid: pGEMEX-MMP-3(DC)E202Q / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08254, stromelysin 1
#2: Protein Metalloproteinase inhibitor 1 / TIMP-1 / Erythroid potentiating activity / EPA / Tissue inhibitor of metalloproteinases / ...TIMP-1 / Erythroid potentiating activity / EPA / Tissue inhibitor of metalloproteinases / Fibroblast collagenase inhibitor / Collagenase inhibitor


Mass: 14269.307 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMP1 OR TIMP OR CLGI / Plasmid: pET3a-N-TIMP-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01033

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-separated NOESY; HNCA; HNCO; HN(CO)CA
121(H)CCH-TOCSY; (H)CCH-COSY;
23315N-separated NOESY; HNCA; HNCO; HN(CO)CA
24415N-separated NOESY
15215N-separated NOESY
26515N-separated NOESY
276coupled 15N-HSQC; coupled 13C-HSQC; Ha-coupled HNCA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM MMP-3 U-15N, 13C; 0.8mM N-TIMP-1; 20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide; 93% H2O, 7% D2O93% H2O/7% D2O
20.5mM MMP-3 U-2H, 15N; 0.5mM N-TIMP-1; 20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide; 93% H2O, 7% D2O93% H2O/7% D2O
30.66mM N-TIMP-1 U-15N, 13C; 0.66mM MMP-3(E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O93% H2O/7% D2O
40.3mM 98% 2H/15N N-TIMP-1; 0.3mM MMP-3 (E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O93% H2O/7% D2O
50.3mM 98% 2H/15N N-TIMP-1; 0.3mM (15N-IV, 15N, 13C-L)MMP-3(E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O93% H2O/7% D2O
60.3mM 98% 2H/15N N-TIMP-1; 0.3mM (15N-IV, 15N, 13C-L)MMP-3(E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O 5% PEG(C12E6)/1-hexanol93% H2O; 7% D2O 5% PEG(C12E6)/1-hexanol
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide 6.6 ambient 310 K
220mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2;1mM Sodium Azide 6.7 ambient 307 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian UNITYPLUSVarianUNITYPLUS7202
Bruker DRXBrukerDRX7503
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
XPLORNIHBRUNGERrefinement
PALESSGI Irix 6.2ZWECKSTETTER AND BAXdata analysis
Module1DOSSET ET ALdata analysis
RefinementMethod: RIGID BODY MINIMIZATION, RESTRAINED SIMULATED ANNEALING
Software ordinal: 1
Details: STRUCTURES WERE CALCULATED USING XPLOR-NIH. REFINEMENTS WERE CARRIED OUT FIRST BY RIGID BODY MINIMIZATION (CLORE(2000) PROC.NATL.ACAD.SCI. 97, 9021-9025) FOLLOWED BY RESTRAINED SIMULATED ...Details: STRUCTURES WERE CALCULATED USING XPLOR-NIH. REFINEMENTS WERE CARRIED OUT FIRST BY RIGID BODY MINIMIZATION (CLORE(2000) PROC.NATL.ACAD.SCI. 97, 9021-9025) FOLLOWED BY RESTRAINED SIMULATED ANNEALING (WANG ET AL. EMBO J. (2000) 19,5635-5649). THE CRYSTAL STRUCTURE OF THE COMPLEX BY BODE ET AL. (NATURE (1997), 389, 77-81; PDB CODE: 1UEA) HAS BEEN USED AS A STARTING POINT WITH PROTONS ATTACHED AND TAKING ONLY N-TERMINAL 126 RESIDUES OF TIMP-1. INTERFACIAL SIDE CHAINS OF THE FOLLOWING RESIDUES WERE ALLOWED TO BE FLEXIBLE: CHAIN A (MMP-3(DC)): 162-169,198-202, 205-206, 211 AND 221-223; CHAIN B (N-TIMP-1): 302-304, 329, 333-335,366-369; A TOTAL OF 49 NOE (46 INTERMOLECULAR AND 3 INTRAMOLECULAR) 75 NH DIPOLAR COULINGS FOR N-TIMP-1, 19 NH DIPOLAR COUPLINGS AND 8 CaHa DIPOLAR COUPLINGS FOR MMP-3 WERE USED FOR REFINEMENT. TARGET FUNCTIONS INCLUDE TERMS FOR NOE RESTRAINTS, DIPOLAR COUPLING RESTRAINTS AND RADIUS OF GYRATION. ALSO, MODULE ( DOSSET ET AL. J. BIOMOL. NMR, (2001),20,223-231) AND PALES (ZWECKSTETTER AND BAX, J. AM. CHEM. SOC (2000), 122, 3791-3792) WERE USED FOR EVALUATING THE ORIENTATION AND STRUCTURES.
NMR ensembleConformer selection criteria: lowest energy structure / Conformers calculated total number: 25 / Conformers submitted total number: 1

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