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- PDB-7s7m: Complex of tissue inhibitor of metalloproteinases-1 (TIMP-1) muta... -

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Basic information

Entry
Database: PDB / ID: 7s7m
TitleComplex of tissue inhibitor of metalloproteinases-1 (TIMP-1) mutant (L34G/M66D/T98G/P131S/Q153N) 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


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. / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Peptidoglycan binding-like ...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 / 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 / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Metalloproteinase inhibitor 1 / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCoban, M. / Raeeszadeh-Sarmazdeh, M. / Sankaran, B. / Hockla, A. / 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

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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)40,2607
Polymers40,0092
Non-polymers2515
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-76 kcal/mol
Surface area15460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.280, 69.280, 318.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
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

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Components

#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: 20592.516 Da / Num. of mol.: 1 / Mutation: L34G, M66D, T98G, P131S, Q153N
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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M ammonium acetate, 0.1 M Bis-Tris-HCl, pH 5.5, 17% w/v PEG10000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999995 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 3→15.63 Å / Num. obs: 9900 / % possible obs: 94.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 77.47 Å2 / CC1/2: 0.943 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.084 / Rrim(I) all: 0.152 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
6.33-15.634.10.04916.316840.9980.0270.05699.7
5.08-6.3330.079.617280.990.0460.08499.8
4.46-5.082.80.07810.616930.9840.0540.09699.8
4.06-4.462.70.1148.316860.9650.080.1499.88
3.77-4.062.60.216.714930.5140.1620.26886.25
3.55-3.772.80.2525.214300.7510.180.31284.57
3.38-3.552.910.4073.613460.6180.2870.50178.99
3.23-3.383.20.4012.416980.780.2610.48199.07
3.11-3.233.40.5821.616820.6760.3710.69399.06
3-3.113.40.7721.216650.4690.4850.91599.64

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Processing

Software
NameVersionClassification
PHENIX1.15rc3_3435refinement
iMOSFLM7.2.2data reduction
Aimless0.7.2data scaling
MOLREP11.7.01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UEA

1uea


Resolution: 3→15.63 Å / SU ML: 0.4212 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4598
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 465 5.02 %random
Rwork0.2023 ---
obs0.2047 9263 94.57 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 79.87 Å2
Refinement stepCycle: LAST / Resolution: 3→15.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 5 50 2560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772576
X-RAY DIFFRACTIONf_angle_d0.98023519
X-RAY DIFFRACTIONf_chiral_restr0.0594392
X-RAY DIFFRACTIONf_plane_restr0.0072454
X-RAY DIFFRACTIONf_dihedral_angle_d10.80261482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.430.36651560.28462958X-RAY DIFFRACTION98.92
3.43-4.310.27221380.23282596X-RAY DIFFRACTION84.93
4.31-15.630.20631710.16283244X-RAY DIFFRACTION99.68
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)
12.705410395350.9850312162740.1209179280995.651341783271.813033113914.43272133187-0.04381048992940.04049573136370.07930855653580.0866077272308-0.06215037323010.5734971602660.570657567664-0.7518420271310.139105794850.516434644219-0.05108468169230.1209094202030.663267184740.1440806681150.63298414233610.009029847532.7486420859170.150895285
23.916610283071.29220881446-0.7533019857492.356842269392.118854840773.18180693471-0.240683060455-0.8577122033070.8420470367620.7209746832750.475296331211-0.09067649665930.945197848827-0.0771018746183-0.492361838030.724709587861-0.06221073359570.03480697203351.035873902060.1900901787790.62959691045423.118763764940.3385661924183.016635082
34.77888441706-5.475631351050.1751511995456.66884439743-0.8530312419131.12109348553-0.03537993652340.7429166945431.585942288270.633083240170.452555075154-0.701460023851-0.8530074170340.6620927764660.7502838931391.052525967640.08056869648490.1360381083650.5003548347860.2179572451710.54173194869526.057896174942.626477224174.474951287
44.800758270530.7660613895981.964702921539.17095647456-2.303212824943.849924271590.1420523572830.2267370138560.5487649537940.649724910233-0.104844015996-0.352398202313-0.241680455566-0.640648418239-0.01291729165710.606482735520.06321208916490.2235787254930.6023408714350.06249173530380.455213936618.450356790139.8301166693171.849255615
53.91809118763-3.214095359851.36811366159.57086134252-2.938685284360.980539657821-0.255095738167-0.04055174283350.5388176381730.8076132397690.886421201889-0.407535568190.623427454345-0.991928550123-0.4638804251480.744030998230.03894387453910.1441089124670.44191752310.2579332640270.37230700271718.864945725534.084341463166.952166102
64.090644047244.10912005202-1.393918311597.610899306281.088968540953.00102571532-0.9798529506411.561288011310.169686988359-0.2424066906250.758775176604-0.146482382782-0.521111549944-0.4165391957270.06926026373490.7856955360330.02228482878440.1811935616620.6886340789880.311173065850.83353626532328.314283785829.1061069716163.108571643
75.93157624973.45464673995-2.17952902862.85897113695-1.957767177711.39750363361.56085808869-0.3234226001660.152173844637-1.12483426203-0.368152736949-0.0995924196584-0.9039788460190.119244824938-0.5765477067141.04443251322-0.03893802599150.06869274099080.5167558023020.1482955811680.7010769560426.932363192537.7078937736161.518984831
84.44109761102-1.882244376332.719061794423.088221821.376763859349.38556468909-0.2120982348041.360477336310.326438547412-0.5182309684190.217740487973-0.2192022383391.00091499539-0.37239278238-0.260222340070.572990128144-0.1565826839630.05961298592610.7044125811310.1725897581720.86508603239420.073371760126.6668402121158.351298977
95.146268344330.9775186245951.794977369674.72170424562-1.892294425865.265420936350.161959915562-0.203334394388-0.3733638624180.5913621571310.0915803054761-0.2543006106170.09613147503950.049416583082-0.1253986767460.8611150614780.0210607639223-0.04047640271290.4418394061070.1000287267450.43823155825641.330284469436.1329737745179.598663448
102.04307584339-4.941894223-4.258543576165.162348370964.406519482313.88770508898-0.3418468961120.680104562105-1.19002638831.46633782461-0.1594562751210.6119540521330.235291779525-0.1603077188490.7365971732011.19720623139-0.245067266073-0.0861485114520.4272103618130.1824195366330.53728608713943.042127867739.6539479065179.692695076
114.034893977482.7365051658-1.785491081268.50956990712-6.397666882939.475898370740.286933273812-0.1027402489240.3355096462920.303195946304-0.4694988447530.5171734117060.861122485611-0.994257558274-1.13437932040.813517798623-0.172662672145-0.03674823430450.5115711936510.1510732501560.50582059864337.272927856839.2410116365180.523798437
125.826253927280.0558914356833-1.570903338846.54135743986-2.986068687042.22993745863-0.1845322836020.139708862413-0.213847303323-0.300344329838-0.87187522261-1.446628037071.031533189351.040597237950.8692245083070.7211898757110.0185445705496-0.03265736086810.6320981976920.2008712575360.59006487217350.640818158543.4424394447169.262288885
136.68707996466-0.8256001560173.190412785382.44413897017-0.7231686156916.223007563430.2280638691180.593433656447-0.1942797749361.177619524770.3292747226790.453597092178-0.915259259694-0.830349765908-0.3129500356860.964094062191-0.0501812910875-0.1312192051080.5592012878980.2201128267480.62752902928835.838511819553.3974890889164.771983632
146.006276565570.903164014308-0.3175648910195.18506792946-4.818409015724.55823186815-0.147566437681-0.13270148366-0.3429416063540.567961026772-0.0606862173977-0.838214565255-1.274291606660.260218903385-0.03789943880710.998217168662-0.23742897538-0.2031642647190.4668551376280.1624589110790.74287859811444.718948763755.5959885209163.622196334
159.806165709610.5039894329683.168084001411.64022462312.781625359035.39611015944-0.9061796971130.1185957879240.03422754587771.335230469471.13458075879-0.574435480262-1.559929561540.0485368295191-0.2795565628990.8147415724410.06195438086090.06506327027680.3601991259590.1150881922760.83030717418743.623124767161.0854528106165.288994203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 88 through 147 )
2X-RAY DIFFRACTION2chain 'A' and (resid 148 through 157 )
3X-RAY DIFFRACTION3chain 'A' and (resid 158 through 167 )
4X-RAY DIFFRACTION4chain 'A' and (resid 168 through 194 )
5X-RAY DIFFRACTION5chain 'A' and (resid 195 through 207 )
6X-RAY DIFFRACTION6chain 'A' and (resid 208 through 217 )
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 227 )
8X-RAY DIFFRACTION8chain 'A' and (resid 228 through 247 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 81 )
10X-RAY DIFFRACTION10chain 'B' and (resid 82 through 90 )
11X-RAY DIFFRACTION11chain 'B' and (resid 91 through 101 )
12X-RAY DIFFRACTION12chain 'B' and (resid 102 through 117 )
13X-RAY DIFFRACTION13chain 'B' and (resid 118 through 158 )
14X-RAY DIFFRACTION14chain 'B' and (resid 159 through 170 )
15X-RAY DIFFRACTION15chain 'B' and (resid 171 through 179 )

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