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- PDB-6mav: Complex of tissue inhibitor of metalloproteinase-1 (TIMP-1) mutan... -

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Basic information

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


regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / stromelysin 1 / peptidase inhibitor activity / connective tissue replacement involved in inflammatory response wound healing / negative regulation of trophoblast cell migration / negative regulation of membrane protein ectodomain proteolysis / 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 / peptidase inhibitor activity / connective tissue replacement involved in inflammatory response wound healing / negative regulation of trophoblast cell migration / negative regulation of membrane protein ectodomain proteolysis / 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 / EGFR Transactivation by Gastrin / extracellular matrix / Degradation of the extracellular matrix / response to hormone / extracellular matrix organization / platelet alpha granule lumen / cytokine activity / response to cytokine / Post-translational protein phosphorylation / positive regulation of protein-containing complex assembly / growth factor activity / metalloendopeptidase activity / response to peptide hormone / cellular response to reactive oxygen species / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / metallopeptidase activity / Platelet degranulation / peptidase activity / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / cellular response to lipopolysaccharide / 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 / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleus / cytoplasm
Similarity search - Function
Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / 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 ...Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / 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) / Alpha-Beta Complex / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsRaeeszadeh-Sarmazdeh, M. / Radisky, E.
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)DOD W81XWH-16-2-0030 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.
History
DepositionAug 28, 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
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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

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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)39,8157
Polymers39,5642
Non-polymers2515
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-80 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.703, 69.703, 321.326
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-210-

HOH

21B-218-

HOH

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Components

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


Mass: 18887.029 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 Metalloproteinase inhibitor 1 / Matrix metalloproteinase inhibitor / 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: 20676.740 Da / Num. of mol.: 1 / Mutation: L34G
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
#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 / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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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: 2.96 Å3/Da / Density % sol: 58.43 %
Crystal growTemperature: 298 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) PEG 10,000
PH range: 5.5-6.5

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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: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→52.59 Å / Num. obs: 19911 / % possible obs: 99.94 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06602 / Rrim(I) all: 0.06901 / Net I/σ(I): 19.1
Reflection shellResolution: 2.37→2.49 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.7907 / Mean I/σ(I) obs: 3.09 / Num. unique obs: 1928 / CC1/2: 0.933 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UEA

1uea


Resolution: 2.37→52.588 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.89
RfactorNum. reflection% reflection
Rfree0.2978 940 4.86 %
Rwork0.2171 --
obs0.2211 19361 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.76 Å2 / Biso mean: 77.4715 Å2 / Biso min: 39.66 Å2
Refinement stepCycle: final / Resolution: 2.37→52.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 5 33 2681
Biso mean--69.81 71.31 -
Num. residues----335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012724
X-RAY DIFFRACTIONf_angle_d1.3493697
X-RAY DIFFRACTIONf_chiral_restr0.051401
X-RAY DIFFRACTIONf_plane_restr0.008477
X-RAY DIFFRACTIONf_dihedral_angle_d16.369968
LS refinement shell

Refine-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 (%)
2.3701-2.4950.44441340.3612503263795
2.495-2.65140.40361200.3352463258394
2.6514-2.85610.4231070.32232580268797
2.8561-3.14340.38771340.29742602273697
3.1434-3.59820.35621310.26282634276598
3.5982-4.5330.27131560.18822693284999
4.533-52.60070.22861580.15392946310499
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)
17.9948-3.34632.36634.7825-0.80413.8298-0.1619-0.47660.47420.05740.151-0.6436-0.5691-0.139-0.02860.6927-0.1281-0.05020.5472-0.18250.808222.121336.421613.5715
22.66251.36070.06177.8571-0.04434.26330.2350.319-0.4877-0.9635-0.3668-1.16680.60411.53850.06660.70750.0823-0.06020.7253-0.20190.708525.315724.06329.5945
34.1940.7272-0.33785.49012.46442.0710.1064-1.0313-0.76920.9218-0.25640.33450.26120.42990.02710.9607-0.2-0.20450.4478-0.12260.441813.008222.250819.5879
44.0189-0.6934-0.01893.4099-2.09171.5778-0.04580.2073-0.4014-0.1943-0.19160.2156-0.0928-0.15470.20550.759-0.0222-0.06710.4232-0.21160.640112.984921.64076.5202
52.63290.10280.4944.35860.8730.9525-0.11590.6430.0338-0.27220.3854-0.58070.6840.776-0.01821.03230.01340.02210.7378-0.18130.621510.983522.6199-1.586
63.3960.4781-1.9922.01010.47133.89940.20190.5415-0.0713-0.87920.01161.1008-1.6412-0.12411.24471.1277-0.02770.06020.3618-0.21010.69313.369338.34031.5545
70.54540.74640.28574.53942.3763.61380.0321-0.52830.14581.0554-0.25120.31080.4093-0.15860.0920.9424-0.11850.0970.5022-0.11940.5941-6.430616.379115.5044
86.6004-1.95140.93353.08551.81655.1912-0.7906-0.24290.25980.84970.4493-0.1942-0.00030.24450.24561.0805-0.10950.09090.6014-0.210.6207-4.222131.070425.983
92.8770.8407-2.61291.45261.61767.38960.9753-0.2990.40022.0443-0.95490.67910.1882-2.4681-0.0191.0414-0.28520.37180.7862-0.14850.9466-15.454116.783525.7378
105.4774-0.2279-2.09061.7672-0.30193.11560.2266-0.081.26570.52520.00330.2348-0.62060.0591-0.42120.9776-0.04280.06730.4319-0.13040.6695-5.162229.912517.589
112.54171.8831-0.8115.69242.82433.4261-0.0449-0.92250.05290.7649-0.3051-1.18210.13310.4094-0.32070.9989-0.05820.02370.3634-0.07780.467-4.211420.157521.0685
122.65421.0017-0.09776.37040.17683.70340.13350.3278-0.44650.5573-0.95061.69660.5794-2.07420.65360.8138-0.11550.21730.6161-0.22820.7852-15.776813.980610.7595
132.82282.62030.98688.4205-1.54956.72731.1423-1.1093-0.17321.8756-0.78151.2280.24171.4496-0.50461.4-0.00130.1350.4825-0.15020.7444-3.13152.86411.7344
142.3837-1.95272.16621.5954-1.76951.9619-0.49680.02811.08550.41660.0830.0398-0.05390.48020.17461.12110.0875-0.14340.47-0.1260.74875.13292.67742.8208
156.67081.3319-0.55345.59580.961.6612-0.10191.0898-0.0124-0.92890.62730.03550.42590.2774-0.56841.0829-0.1940.07920.5631-0.06220.5628-1.71611.38680.6616
164.02661.2332-0.50762.42150.13853.9411-0.3209-0.0583-0.07050.0498-0.15350.1270.616-0.53270.47471.0645-0.0609-0.00820.4377-0.13370.6315-10.27722.62994.5834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 87 through 101 )A87 - 101
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 147 )A102 - 147
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 181 )A148 - 181
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 217 )A182 - 217
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 235 )A218 - 235
6X-RAY DIFFRACTION6chain 'A' and (resid 236 through 247 )A236 - 247
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 23 )B1 - 23
8X-RAY DIFFRACTION8chain 'B' and (resid 24 through 42 )B24 - 42
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 59 )B43 - 59
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 82 )B60 - 82
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 101 )B83 - 101
12X-RAY DIFFRACTION12chain 'B' and (resid 102 through 123 )B102 - 123
13X-RAY DIFFRACTION13chain 'B' and (resid 124 through 131 )B124 - 131
14X-RAY DIFFRACTION14chain 'B' and (resid 132 through 143 )B132 - 143
15X-RAY DIFFRACTION15chain 'B' and (resid 144 through 158 )B144 - 158
16X-RAY DIFFRACTION16chain 'B' and (resid 159 through 179 )B159 - 179

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