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- PDB-2j0t: Crystal Structure of the Catalytic Domain of MMP-1 in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 2j0t
TitleCrystal Structure of the Catalytic Domain of MMP-1 in Complex with the Inhibitory Domain of TIMP-1
Components
  • INTERSTITIAL COLLAGENASE
  • METALLOPROTEINASE INHIBITOR 1
KeywordsHYDROLASE / EXTRACELLULAR MATRIX / ERYTHROCYTE MATURATION / AUTOCATALYTIC CLEAVAGE / COLLAGEN DEGRADATION
Function / homology
Function and homology information


negative regulation of metallopeptidase activity / interstitial collagenase / regulation of integrin-mediated signaling pathway / negative regulation of membrane protein ectodomain proteolysis / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / negative regulation of endopeptidase activity / negative regulation of catalytic activity ...negative regulation of metallopeptidase activity / interstitial collagenase / regulation of integrin-mediated signaling pathway / negative regulation of membrane protein ectodomain proteolysis / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / negative regulation of endopeptidase activity / negative regulation of catalytic activity / cellular response to UV-A / cellular response to peptide / peptidase inhibitor activity / cartilage development / Basigin interactions / Activation of Matrix Metalloproteinases / Interleukin-10 signaling / Collagen degradation / collagen catabolic process / basement membrane / extracellular matrix disassembly / response to hormone / Degradation of the extracellular matrix / response to cytokine / extracellular matrix organization / extracellular matrix / platelet alpha granule lumen / cytokine activity / Post-translational protein phosphorylation / growth factor activity / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / response to peptide hormone / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / peptidase activity / protease binding / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding
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 / 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 / Interstitial collagenase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsIyer, S. / Wei, S. / Brew, K. / Acharya, K.R.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structure of the Catalytic Domain of Matrix Metalloproteinase-1 in Complex with the Inhibitory Domain of Tissue Inhibitor of Metalloproteinase-1.
Authors: Iyer, S. / Wei, S. / Brew, K. / Acharya, K.R.
History
DepositionAug 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERSTITIAL COLLAGENASE
B: INTERSTITIAL COLLAGENASE
C: INTERSTITIAL COLLAGENASE
D: METALLOPROTEINASE INHIBITOR 1
E: METALLOPROTEINASE INHIBITOR 1
F: METALLOPROTEINASE INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,55121
Polymers99,7986
Non-polymers75315
Water73941
1
A: INTERSTITIAL COLLAGENASE
D: METALLOPROTEINASE INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5177
Polymers33,2662
Non-polymers2515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-73 kcal/mol
Surface area13900 Å2
MethodPISA
2
B: INTERSTITIAL COLLAGENASE
E: METALLOPROTEINASE INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5177
Polymers33,2662
Non-polymers2515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-74.5 kcal/mol
Surface area13790 Å2
MethodPISA
3
C: INTERSTITIAL COLLAGENASE
F: METALLOPROTEINASE INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5177
Polymers33,2662
Non-polymers2515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-72.5 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.098, 67.850, 86.241
Angle α, β, γ (deg.)90.00, 100.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein INTERSTITIAL COLLAGENASE / MATRIX METALLOPROTEINASE-1 / MMP-1 / FIBROBLAST COLLAGENASE


Mass: 18996.736 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN, RESIDUES 101-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03956, interstitial collagenase
#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 / TISSUE INHIBITOR OF METALLOPROTEINASE-1


Mass: 14269.307 Da / Num. of mol.: 3 / Fragment: N-TERMINAL INHIBITORY DOMAIN, RESIDUES 24-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01033
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCLEAVES COLLAGENS OF TYPES I, II, AND III AT ONE SITE IN THE HELICAL DOMAIN. ALSO CLEAVES COLLAGENS ...CLEAVES COLLAGENS OF TYPES I, II, AND III AT ONE SITE IN THE HELICAL DOMAIN. ALSO CLEAVES COLLAGENS OF TYPES VII AND X. COMPLEXES WITH METALLOPROTEINASES (SUCH AS COLLAGENASES) AND IRREVERSIBLY INACTIVATES THEM. ALSO MEDIATES ERYTHROPOIESIS IN VITRO; BUT, UNLIKE IL-3, IT IS SPECIES-SPECIFIC, STIMULATING THE GROWTH AND DIFFERENTIATION OF ONLY HUMAN AND MURINE ERYTHROID PROGENITORS.
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: 46.1 %
Crystal growpH: 7.5
Details: 10% PEG 8000, 8% ETHYLENE GLYCOL, 0.1M HEPES (PH 7.5).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 23, 2002 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.54→40 Å / Num. obs: 29526 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 59.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.3
Reflection shellResolution: 2.54→2.63 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1CGL AND 1UEA

1cgl

1uea


Resolution: 2.54→23 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.892 / SU B: 29.759 / SU ML: 0.294 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.118 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED AS ALANINES OR GLYCINES.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 997 3.4 %RANDOM
Rwork0.248 ---
obs0.249 28349 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.04 Å2
Baniso -1Baniso -2Baniso -3
1-2.67 Å20 Å20.42 Å2
2---0.9 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 2.54→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6491 0 15 41 6547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216681
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8921.9279079
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4815848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44423.498323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63515942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9541540
X-RAY DIFFRACTIONr_chiral_restr0.0590.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025329
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1690.22842
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.24527
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.2169
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1331.54285
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.2426656
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.26532740
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.4214.52423
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.54→2.6 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 67
Rwork0.351 2100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.5334-3.0383-0.294410.32213.035816.52360.4371.0973-0.0299-1.3495-0.53350.6084-0.2007-1.55540.09660.02840.1952-0.04620.21390.0193-0.166641.39086.4338.7795
26.65421.0856-0.6793.27110.09156.0048-0.0438-0.6108-0.2802-0.1123-0.1864-0.1905-0.02470.17120.2302-0.29480.1401-0.02-0.25730.1202-0.268756.3555-0.275329.7194
34.7684-1.6751-1.00757.11213.061719.59780.40750.82260.1178-0.5442-0.02780.5875-0.645-1.4788-0.37970.03110.31520.06620.07770.0897-0.0514-64.54165.07767.8607
45.38040.15010.21575.04571.10234.75720.3416-0.31210.0852-0.3096-0.3565-0.5234-0.260.18910.0149-0.17090.12360.0579-0.16910.1256-0.1934-49.36110.122229.1446
54.8763-2.11552.404812.5281-0.318910.5250.39560.98790.2381-1.1684-0.34130.67580.6038-0.0389-0.05420.09970.2610.04130.00610.0797-0.0065-12.69526.00668.9589
66.15580.58041.63947.5571-2.98059.27760.0825-0.34610.60980.1924-0.5738-0.7084-0.86260.8260.4913-0.06910.14230.0477-0.06470.0711-0.0692.1642-2.242229.0334
72.58610.1221-0.26280.0236-0.03640.059-0.0639-0.41120.18020.02460.03930.0024-0.0137-0.02870.0246-0.00510.24490.01750.00210.00250.0005-5.489-1.688227.427
83.7515-0.0656-0.00950.1792-0.06980.4003-0.1706-0.1866-0.1125-0.03620.0906-0.0109-0.04810.08160.0799-0.00060.0363-0.00240.00170.0025-0.001117.0125-1.034722.4428
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D1 - 124
2X-RAY DIFFRACTION2A105 - 265
3X-RAY DIFFRACTION3E1 - 124
4X-RAY DIFFRACTION4B105 - 266
5X-RAY DIFFRACTION5F1 - 124
6X-RAY DIFFRACTION6C105 - 263
7X-RAY DIFFRACTION7A1266 - 1270
8X-RAY DIFFRACTION7B1267 - 1271
9X-RAY DIFFRACTION7C1264 - 1268
10X-RAY DIFFRACTION8A2001 - 2018
11X-RAY DIFFRACTION8B2001 - 2009
12X-RAY DIFFRACTION8C2001 - 2008
13X-RAY DIFFRACTION8D2001 - 2003
14X-RAY DIFFRACTION8E2001
15X-RAY DIFFRACTION8F2001 - 2002

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