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- PDB-6clz: MT1-MMP HPX domain with Blade 4 Loop Bound to Nanodiscs -

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Basic information

Entry
Database: PDB / ID: 6clz
TitleMT1-MMP HPX domain with Blade 4 Loop Bound to Nanodiscs
Components
  • Apolipoprotein A-I
  • Matrix metalloproteinase-14
KeywordsLIPID BINDING PROTEIN / MT1-MMP / MMP-14 / Nanodisc / lipids / peripheral membrane protein / protease domain
Function / homology
Function and homology information


membrane-type matrix metalloproteinase-1 / negative regulation of GDF15-GFRAL signaling pathway / positive regulation of macrophage migration / craniofacial suture morphogenesis / macropinosome / Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle ...membrane-type matrix metalloproteinase-1 / negative regulation of GDF15-GFRAL signaling pathway / positive regulation of macrophage migration / craniofacial suture morphogenesis / macropinosome / Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / negative regulation of response to cytokine stimulus / protein oxidation / response to odorant / regulation of intestinal cholesterol absorption / vitamin transport / chondrocyte proliferation / head development / blood vessel endothelial cell migration / cholesterol import / astrocyte cell migration / TGFBR3 PTM regulation / negative regulation of heterotypic cell-cell adhesion / ABC transporters in lipid homeostasis / tissue remodeling / apolipoprotein A-I receptor binding / apolipoprotein receptor binding / high-density lipoprotein particle binding / negative regulation of cell adhesion molecule production / negative regulation of cytokine production involved in immune response / HDL assembly / negative regulation of very-low-density lipoprotein particle remodeling / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / negative regulation of focal adhesion assembly / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of protein processing / positive regulation of phospholipid efflux / Chylomicron remodeling / cellular response to lipoprotein particle stimulus / Chylomicron assembly / endochondral ossification / high-density lipoprotein particle clearance / phospholipid efflux / chylomicron / high-density lipoprotein particle remodeling / positive regulation of cholesterol metabolic process / reverse cholesterol transport / lipid storage / phospholipid homeostasis / high-density lipoprotein particle assembly / chemorepellent activity / embryonic cranial skeleton morphogenesis / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transfer activity / cholesterol transport / high-density lipoprotein particle / very-low-density lipoprotein particle / intermediate filament cytoskeleton / regulation of Cdc42 protein signal transduction / endothelial cell proliferation / zymogen activation / HDL remodeling / cholesterol efflux / Scavenging by Class A Receptors / triglyceride homeostasis / adrenal gland development / positive regulation of B cell differentiation / negative regulation of interleukin-1 beta production / negative chemotaxis / cholesterol binding / cholesterol biosynthetic process / branching morphogenesis of an epithelial tube / positive regulation of myotube differentiation / amyloid-beta formation / positive regulation of Rho protein signal transduction / Activation of Matrix Metalloproteinases / metalloaminopeptidase activity / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / endocytic vesicle / negative regulation of Notch signaling pathway / positive regulation of cholesterol efflux / negative regulation of tumor necrosis factor-mediated signaling pathway / response to mechanical stimulus / Scavenging of heme from plasma / regulation of protein localization to plasma membrane / cholesterol metabolic process / Retinoid metabolism and transport / ovarian follicle development / positive regulation of stress fiber assembly / Degradation of the extracellular matrix / heat shock protein binding / endocytic vesicle lumen / extracellular matrix organization / positive regulation of substrate adhesion-dependent cell spreading
Similarity search - Function
Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / 4 Propeller / Hemopexin / Hemopexin-like domain / PGBD superfamily / Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / Hemopexin, conserved site ...Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / 4 Propeller / Hemopexin / Hemopexin-like domain / PGBD superfamily / Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / 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. / Mainly Beta
Similarity search - Domain/homology
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Apolipoprotein A-I / Matrix metalloproteinase-14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsMarcink, T.C. / Van Doren, S.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA098799 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR022341 United States
CitationJournal: Structure / Year: 2019
Title: MT1-MMP Binds Membranes by Opposite Tips of Its beta Propeller to Position It for Pericellular Proteolysis.
Authors: Marcink, T.C. / Simoncic, J.A. / An, B. / Knapinska, A.M. / Fulcher, Y.G. / Akkaladevi, N. / Fields, G.B. / Van Doren, S.R.
History
DepositionMar 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix metalloproteinase-14
B: Apolipoprotein A-I
C: Apolipoprotein A-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,023223
Polymers72,9563
Non-polymers148,067220
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: The protein's NMR rotational correlation time increased upon addition of nanodiscs indicating interactions between the molecules. Furthermore, ultra-centrifugation, fluorescence, and ...Evidence: The protein's NMR rotational correlation time increased upon addition of nanodiscs indicating interactions between the molecules. Furthermore, ultra-centrifugation, fluorescence, and mutagenesis were used to demonstrate the association with vesicles in the orientation determined by NMR.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Matrix metalloproteinase-14 / MMP-14 / MMP-X1 / Membrane-type matrix metalloproteinase 1 / MTMMP1 / Membrane-type-1 matrix ...MMP-14 / MMP-X1 / Membrane-type matrix metalloproteinase 1 / MTMMP1 / Membrane-type-1 matrix metalloproteinase / MT1MMP


Mass: 23131.346 Da / Num. of mol.: 1 / Fragment: residues 316-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP14 / Production host: Escherichia coli (E. coli)
References: UniProt: P50281, membrane-type matrix metalloproteinase-1
#2: Protein Apolipoprotein A-I / ApoA-I / Apolipoprotein A1


Mass: 24912.156 Da / Num. of mol.: 2 / Fragment: residues 79-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02647
#3: Chemical...
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 218 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1HMQC
121isotropic1TROSY
131isotropic1CPMG-HMQC

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Sample preparation

DetailsType: solution
Contents: 20 mM Tris-HCl, 300 mM NaCl, 0.02 % sodium azide, 93 % H2O, 7 % [U-100% 2H] D2O, 90 uM 2H, 13C, 15N MT1-MMP hemopexin-like domain, 180 uM MSP1D1, 14.4 mM PX4, 93% H2O/7% D2O
Details: 300 mM NaCl was used to reduce affinity of HPX to the nanodisc and recover sample. Shaped NMR tubes were used to obtain better spectra.
Label: 2H, 13C, 15N / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMTris-HClnatural abundance1
300 mMNaClnatural abundance1
0.02 %sodium azidenatural abundance1
93 %H2Onatural abundance1
7 %D2O[U-100% 2H]1
90 uMMT1-MMP hemopexin-like domain2H, 13C, 15N1
180 uMMSP1D1natural abundance1
14.4 mMPX4natural abundance1
Sample conditionsDetails: MT1-MMP hemopxin-like domain was along with MSP1D1 and PX4 lipids were in a buffer containing 300 mM NaCl, 0.02% sodium azide, 93% water, 7% D2O, 20 mM Tris-HCl pH 7.2
Ionic strength: 300 mM / Label: NMR Buffer / pH: 7.2 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Brukerprocessing
Analysis2.4CCPNdata analysis
HADDOCKHADDOCK2.1Bonvinstructure calculation
NAMDNAMD2.1 with CUDA GPU processingTheoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaignstructure calculation
NAMDNAMD2.1 with CUDA GPU processingTheoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaignrefinement
RefinementMethod: molecular dynamics / Software ordinal: 5 / Details: restrained molecular dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 15

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