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- PDB-7s7l: Complex of tissue inhibitor of metalloproteinases-1 (TIMP-1) muta... -

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Basic information

Entry
Database: PDB / ID: 7s7l
TitleComplex of tissue inhibitor of metalloproteinases-1 (TIMP-1) mutant (L34G/M66S/E67Y/L133N/S155L) with matrix metalloproteinase-3 catalytic domain (MMP-3cd)
Components
  • Metalloproteinase inhibitor 1
  • Stromelysin-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / metalloproteinase / metalloproteinase inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of metallopeptidase activity / regulation of integrin-mediated signaling pathway / stromelysin 1 / 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 / regulation of integrin-mediated signaling pathway / stromelysin 1 / 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 / regulation of neuroinflammatory response / 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 / negative regulation of reactive oxygen species metabolic process / basement membrane / extracellular matrix disassembly / response to hormone / Degradation of the extracellular matrix / response to cytokine / extracellular matrix organization / EGFR Transactivation by Gastrin / extracellular matrix / cellular response to nitric oxide / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell migration / platelet alpha granule lumen / cytokine activity / cellular response to reactive oxygen species / Post-translational protein phosphorylation / growth factor activity / cellular response to amino acid stimulus / protein catabolic process / positive regulation of protein-containing complex assembly / response to peptide hormone / metalloendopeptidase activity / 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 / protease binding / Interleukin-4 and Interleukin-13 signaling / 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 / extracellular region / zinc ion binding / 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. / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Hemopexin, conserved site ...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. / 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 / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
ACETATE ION / Metalloproteinase inhibitor 1 / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsCoban, M. / Raeeszadeh-Sarmazdeh, M. / Hockla, A. / Sankaran, B. / Radisky, E.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA205471 United States
Department of Defense (DOD, United States)W81XWH-16-2-0030 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Engineering of tissue inhibitor of metalloproteinases TIMP-1 for fine discrimination between closely related stromelysins MMP-3 and MMP-10.
Authors: Raeeszadeh-Sarmazdeh, M. / Coban, M. / Mahajan, S. / Hockla, A. / Sankaran, B. / Downey, G.P. / Radisky, D.C. / Radisky, E.S.
History
DepositionSep 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,76612
Polymers40,1102
Non-polymers65610
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-14 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.332, 69.332, 312.215
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-307-

TRS

21B-201-

SO4

31B-203-

ACT

41A-409-

HOH

51B-336-

HOH

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 19416.529 Da / Num. of mol.: 1 / Fragment: Catalytic domain (UNP residues 100-272)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP3, STMY1 / Cell line (production host): HEK-293 FreeStyle / Production host: Homo sapiens (human) / References: UniProt: P08254, stromelysin 1
#2: Protein Metalloproteinase inhibitor 1 / Erythroid-potentiating activity / EPA / Fibroblast collagenase inhibitor / Collagenase inhibitor / ...Erythroid-potentiating activity / EPA / Fibroblast collagenase inhibitor / Collagenase inhibitor / Tissue inhibitor of metalloproteinases 1 / TIMP-1


Mass: 20693.707 Da / Num. of mol.: 1 / Mutation: L34G, M66S, E67Y, L133N, S155L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMP1, CLGI, TIMP / Cell line (production host): HEK-293 FreeStyle / Production host: Homo sapiens (human) / References: UniProt: P01033

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Non-polymers , 8 types, 89 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / 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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.82 Å3/Da / Density % sol: 56.32 % / Description: 3D well-formed hexagon
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M Bis-Tris pH 6.5, 25% w/v PEG 3350 Anatrace-Microlytic Top96 #65
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99994 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 2.34→47.6 Å / Num. obs: 19561 / % possible obs: 98.2 % / Redundancy: 13.7 % / Biso Wilson estimate: 46.18 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.048 / Rrim(I) all: 0.19 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
5.04-47.616.70.10626.422350.9790.0280.1199.8
4-5.0417.40.15925.920520.9930.0390.164100
3.5-4160.2132120110.9870.0540.22100
3.18-3.514.60.25715.119680.9730.0680.266100
2.95-3.1813.20.3111019790.9520.0860.32399.8
2.77-2.9512.50.3767.519070.9190.1060.39198.7
2.64-2.7711.80.5115.519050.8730.1450.53397.3
2.52-2.6411.50.6743.918580.7220.1950.70496.5
2.42-2.52110.8142.918350.6630.2360.8595
2.34-2.4210.70.952.318110.6630.2810.99594.1

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Processing

Software
NameVersionClassification
PHENIX1.15rc3_3435refinement
XDSdata reduction
Aimless0.7.2data scaling
PHASER2.8.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UEA

1uea


Resolution: 2.34→47.6 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.66
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 975 5 %random
Rwork0.2064 ---
obs0.2081 19489 98.02 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å
Displacement parametersBiso max: 134.69 Å2 / Biso mean: 55.6208 Å2 / Biso min: 15.4 Å2
Refinement stepCycle: final / Resolution: 2.34→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2614 0 29 79 2722
Biso mean--55.8 48.53 -
Num. residues----340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3401-2.46350.33381300.2904247495
2.4635-2.61780.31411300.2718247495
2.6178-2.820.29541360.2589256297
2.82-3.10370.27641380.238263699
3.1037-3.55270.2341420.21322685100
3.5527-4.47550.21061440.172737100
4.4755-47.60.21481550.18792946100
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)
10.56410.3887-0.09810.451-0.52721.1855-0.367-0.18970.2516-0.0225-0.0233-0.21880.5309-0.64170.00060.68060.15880.09850.4871-0.1450.442613.1969-44.3033-15.4928
20.08360.12430.06980.18680.03430.85330.04150.19240.11210.0897-0.1276-0.1728-0.26130.6906-0.00380.3672-0.01440.06060.5347-0.13710.724922.3987-20.3635-13.5094
30.0001-0.0224-0.09840.0430.21311.14260.19120.08670.3337-0.033-0.129-0.13250.1684-0.18760.27220.2140.0967-0.03670.4444-0.26130.639221.1208-23.5166-5.1447
40.92780.4990.62820.44450.21820.93380.45450.22050.02880.38370.5322-0.62160.00910.01680.15170.49810.1782-0.10190.5262-0.18830.511522.543-33.3384-5.2774
52.67310.0248-0.71970.01220.03470.4261-0.18960.56980.3654-0.28870.1805-0.25820.0333-0.1037-0.20280.39910.08640.14060.2055-0.09630.325712.8956-22.7508-19.0247
61.78760.5456-0.57180.1783-0.11250.6262-0.11830.35480.13660.03260.0328-0.0216-0.3004-0.31480.05580.36020.04720.02840.3465-0.21160.549112.0782-11.8275-6.9408
71.38750.5561.2410.53970.93041.82160.1756-0.4591-0.35330.3375-0.01660.21270.4542-0.66550.99570.32230.05220.04080.1927-0.12710.19668.6319-28.5192-3.0309
80.260.1405-0.20150.1401-0.1030.14760.25780.39880.3238-0.3949-0.0359-0.16040.07560.24080.03170.38510.01260.05180.36-0.10530.3865-6.327-13.1503-13.5413
91.4761-0.67660.13030.7756-0.090.03430.15820.45480.0020.0599-0.269-0.03580.4928-0.1914-0.12890.4254-0.01130.04070.4052-0.14540.2601-10.491-25.8602-23.4113
100.17770.0322-0.27270.1713-0.2520.8355-0.1983-0.3568-0.1084-0.0796-0.18420.67060.09960.0911-0.07650.8742-0.0130.09080.4646-0.13560.6962-11.7868-31.2386-14.475
110.2237-0.31760.2160.6356-0.42510.2949-0.24510.545-0.1724-0.17490.0269-0.5573-0.13960.0638-0.03610.43470.0260.05340.3622-0.09580.3303-8.7863-20.5593-20.58
120.07410.0903-0.06190.39570.08290.2583-0.0561-0.03280.0989-0.01530.16990.0550.11860.01840.11960.346-0.03420.01660.3403-0.12590.3032-15.4503-10.9768-10.347
130.91060.9246-0.35660.945-0.3640.1416-0.27320.29120.1128-0.31380.2991-0.07080.22140.1310.09620.60230.17430.04830.492-0.13780.44322.1064-2.8352-2.6213
140.95930.4867-0.35260.2777-0.17140.12060.12940.05690.42110.18680.28530.18040.27880.1950.07140.4062-0.0167-0.10260.371-0.05520.3125-5.0443-11.6287-1.0702
150.27430.05790.15110.9873-0.78770.78070.0622-0.1312-0.0282-0.1613-0.3352-0.1587-0.18040.2016-0.07120.36270.0069-0.01080.2693-0.08480.2663-13.7555-2.9949-4.2414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 95 )A83 - 95
2X-RAY DIFFRACTION2chain 'A' and (resid 96 through 109 )A96 - 109
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 125 )A110 - 125
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 134 )A126 - 134
5X-RAY DIFFRACTION5chain 'A' and (resid 135 through 181 )A135 - 181
6X-RAY DIFFRACTION6chain 'A' and (resid 182 through 194 )A182 - 194
7X-RAY DIFFRACTION7chain 'A' and (resid 195 through 247 )A195 - 247
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 16 )B1 - 16
9X-RAY DIFFRACTION9chain 'B' and (resid 17 through 69 )B17 - 69
10X-RAY DIFFRACTION10chain 'B' and (resid 70 through 81 )B70 - 81
11X-RAY DIFFRACTION11chain 'B' and (resid 82 through 101 )B82 - 101
12X-RAY DIFFRACTION12chain 'B' and (resid 102 through 131 )B102 - 131
13X-RAY DIFFRACTION13chain 'B' and (resid 132 through 143 )B132 - 143
14X-RAY DIFFRACTION14chain 'B' and (resid 144 through 158 )B144 - 158
15X-RAY DIFFRACTION15chain 'B' and (resid 159 through 180 )B159 - 180

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