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- PDB-6n9d: Complex of tissue inhibitor of metalloproteinases-1 (TIMP-1) muta... -

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Basic information

Entry
Database: PDB / ID: 6n9d
TitleComplex of tissue inhibitor of metalloproteinases-1 (TIMP-1) mutant (L34G/L133P/L151C/G154A) with matrix metalloproteinase-3 catalytic domain (MMP-3cd)
Components
  • Metalloproteinase inhibitor 1Matrix metalloproteinase inhibitor
  • Stromelysin-1Matrix metallopeptidase
KeywordsHYDROLASE/HYDROLASE inhibitor / tissue inhibitor of metalloproteinases / matrix metalloproteinase / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


Degradation of the extracellular matrix / Extra-nuclear estrogen signaling / Post-translational protein phosphorylation / Interleukin-4 and Interleukin-13 signaling / Interleukin-10 signaling / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / EGFR Transactivation by Gastrin / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / Collagen degradation ...Degradation of the extracellular matrix / Extra-nuclear estrogen signaling / Post-translational protein phosphorylation / Interleukin-4 and Interleukin-13 signaling / Interleukin-10 signaling / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / EGFR Transactivation by Gastrin / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / Collagen degradation / Platelet degranulation / negative regulation of metallopeptidase activity / regulation of integrin-mediated signaling pathway / negative regulation of trophoblast cell migration / peptidase inhibitor activity / stromelysin 1 / positive regulation of oxidative stress-induced cell death / connective tissue replacement involved in inflammatory response wound healing / negative regulation of hydrogen peroxide metabolic process / negative regulation of membrane protein ectodomain proteolysis / cell activation / metalloendopeptidase inhibitor activity / regulation of neuroinflammatory response / cartilage development / negative regulation of catalytic activity / negative regulation of endopeptidase activity / response to amyloid-beta / positive regulation of protein oligomerization / basement membrane / response to organic substance / collagen catabolic process / cellular response to nitric oxide / response to peptide hormone / extracellular matrix disassembly / response to cytokine / metallopeptidase activity / platelet alpha granule lumen / response to hormone / extracellular matrix / cytokine activity / growth factor activity / metalloendopeptidase activity / platelet degranulation / post-translational protein modification / extracellular matrix organization / endopeptidase activity / protease binding / aging / endoplasmic reticulum lumen / cytokine-mediated signaling pathway / proteolysis / serine-type endopeptidase activity / cellular protein metabolic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / zinc ion binding / extracellular space / extracellular exosome / extracellular region
Hemopexin / Peptidase M10A, cysteine switch, zinc binding site / Hemopexin-like domain superfamily / PGBD-like superfamily / Peptidase M10A, catalytic domain / Tissue inhibitor of metalloproteinase, conserved site / Proteinase inhibitor I35b (TIMP), C-terminal / Metallopeptidase, catalytic domain superfamily / Peptidase M10A / Hemopexin-like repeats ...Hemopexin / Peptidase M10A, cysteine switch, zinc binding site / Hemopexin-like domain superfamily / PGBD-like superfamily / Peptidase M10A, catalytic domain / Tissue inhibitor of metalloproteinase, conserved site / Proteinase inhibitor I35b (TIMP), C-terminal / Metallopeptidase, catalytic domain superfamily / Peptidase M10A / Hemopexin-like repeats / Hemopexin-like domain / Hemopexin, conserved site / Metalloproteinase inhibitor 1 / Tissue inhibitor of metalloproteinases-like, OB-fold / Peptidase, metallopeptidase / Peptidoglycan binding-like / Protease inhibitor I35 (TIMP) / Peptidase M10, metallopeptidase / Matrixin / Tissue inhibitor of metalloproteinase / Putative peptidoglycan binding domain / Hemopexin domain signature. / Hemopexin repeat profile. / NTR domain profile. / Matrixins cysteine switch. / Tissue inhibitors of metalloproteinases signature. / Neutral zinc metallopeptidases, zinc-binding region signature. / Netrin domain
Metalloproteinase inhibitor 1 / Stromelysin-1
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsRaeeszadeh-Sarmazdeh, M. / Radisky, E.S. / Sankaran, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer InstituteCA205471 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Directed evolution of the metalloproteinase inhibitor TIMP-1 reveals that its N- and C-terminal domains cooperate in matrix metalloproteinase recognition.
Authors: Raeeszadeh-Sarmazdeh, M. / Greene, K.A. / Sankaran, B. / Downey, G.P. / Radisky, D.C. / Radisky, E.S.
Validation Report
SummaryFull reportAbout validation report
History
DepositionDec 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)39,5117
Polymers39,2602
Non-polymers2515
Water82946
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-81 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)70.031, 70.031, 319.512
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-220-

HOH

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Components

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


Mass: 18595.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP3, STMY1 / Production host: Homo sapiens (human) / References: UniProt: P08254, stromelysin 1
#2: Protein/peptide Metalloproteinase inhibitor 1 / Matrix metalloproteinase inhibitor / Erythroid-potentiating activity / EPA / Fibroblast collagenase inhibitor / Collagenase inhibitor / Tissue inhibitor of metalloproteinases 1 / TIMP-1


Mass: 20664.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMP1, CLGI, TIMP / 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 / Calcium
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Zinc
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium Acetate, 0.1 M Sodium Cacodylate: HCl, pH 6.5 18 % (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.67→43.99 Å / Num. obs: 14162 / % possible obs: 99.99 % / Redundancy: 20.4 % / Biso Wilson estimate: 55.93 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.2469 / Rrim(I) all: 0.2531 / Net I/σ(I): 20.11
Reflection shellResolution: 2.67→2.765 Å / Redundancy: 21.1 % / Mean I/σ(I) obs: 2.16 / Num. unique obs: 1374 / CC1/2: 0.664 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UEA
Resolution: 2.67→43.99 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.2
RfactorNum. reflection% reflection
Rfree0.258 1039 7.35 %
Rwork0.184 --
Obs0.1894 14140 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.22 Å2 / Biso mean: 55.1126 Å2 / Biso min: 23.73 Å2
Refinement stepCycle: final / Resolution: 2.67→43.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2624 0 5 46 2675
Biso mean--51.6 49.17 -
Num. residues----336
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0092706
f_angle_d1.3043680
f_chiral_restr0.049402
f_plane_restr0.007476
f_dihedral_angle_d16.368949
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.81070.40751430.32211798194199
2.8107-2.98680.26591430.254917991942100
2.9868-3.21740.32611460.220718341980100
3.2174-3.5410.31551460.21218401986100
3.541-4.05310.23051480.164818572005100
4.0531-5.10520.2141510.141219042055100
5.1052-43.99630.24091620.16820692231100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.64012.06520.18335.9231-2.16184.55130.1169-0.2328-0.13940.2511-0.3101-1.05750.13990.6620.14430.33390.0236-0.03280.5127-0.09110.518625.403527.138610.2626
24.05480.1535-0.14412.76070.59034.55770.0761-0.032-0.71590.4231-0.3094-0.26010.8346-0.25830.23540.5081-0.0444-0.04330.2821-0.0490.363514.745820.688613.7329
35.81072.808-0.53662.6802-2.11173.0647-0.00550.61960.0606-0.2623-0.00390.73120.2527-0.31080.04550.36320.0455-0.05820.4182-0.13410.475511.167529.57530.5633
45.38521.40130.24893.34911.13054.1670.1652-0.38030.42060.7122-0.27790.26280.3489-0.42640.06860.5745-0.06070.04420.3144-0.07470.31-5.873623.634120.7732
51.0151-1.1303-0.41565.23753.3573.39350.05450.20830.00590.2424-0.06110.04670.34390.0098-0.00690.4813-0.09650.02110.3146-0.02770.3257-5.72669.36588.1272
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
11chain 'A' and (resid 87 through 147 )A87 - 147
22chain 'A' and (resid 148 through 207 )A148 - 207
33chain 'A' and (resid 208 through 247 )A208 - 247
44chain 'B' and (resid 1 through 90 )B1 - 90
55chain 'B' and (resid 91 through 179 )B91 - 179

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