+Open data
-Basic information
Entry | Database: PDB / ID: 6cm1 | |||||||||
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Title | MT1-MMP HPX Domain with Blade 2 Loop Bound to Nanodiscs | |||||||||
Components |
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Keywords | LIPID BINDING PROTEIN / MT1-MMP / MMP-14 / Nanodisc / lipids / peripheral membrane protein / protease domain | |||||||||
Function / homology | Function and homology information membrane-type matrix metalloproteinase-1 / craniofacial suture morphogenesis / positive regulation of macrophage migration / macropinosome / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / positive regulation of hydrolase activity ...membrane-type matrix metalloproteinase-1 / craniofacial suture morphogenesis / positive regulation of macrophage migration / macropinosome / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / regulation of intestinal cholesterol absorption / head development / protein oxidation / vitamin transport / chondrocyte proliferation / cholesterol import / high-density lipoprotein particle binding / astrocyte cell migration / ABC transporters in lipid homeostasis / response to odorant / tissue remodeling / blood vessel endothelial cell migration / negative regulation of heterotypic cell-cell adhesion / apolipoprotein receptor binding / apolipoprotein A-I receptor binding / negative regulation of cytokine production involved in immune response / negative regulation of cell adhesion molecule production / HDL assembly / peptidyl-methionine modification / negative regulation of very-low-density lipoprotein particle remodeling / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / negative regulation of focal adhesion assembly / positive regulation of protein processing / phosphatidylcholine metabolic process / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / lipid storage / Chylomicron assembly / positive regulation of cholesterol metabolic process / phospholipid homeostasis / high-density lipoprotein particle clearance / high-density lipoprotein particle remodeling / endochondral ossification / phospholipid efflux / chemorepellent activity / cholesterol transfer activity / reverse cholesterol transport / high-density lipoprotein particle assembly / very-low-density lipoprotein particle / cholesterol transport / positive regulation of CoA-transferase activity / lipoprotein biosynthetic process / embryonic cranial skeleton morphogenesis / high-density lipoprotein particle / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / zymogen activation / HDL remodeling / endothelial cell proliferation / intermediate filament cytoskeleton / negative regulation of interleukin-1 beta production / Scavenging by Class A Receptors / cholesterol efflux / cholesterol binding / positive regulation of B cell differentiation / negative chemotaxis / adrenal gland development / positive regulation of Rho protein signal transduction / branching morphogenesis of an epithelial tube / positive regulation of myotube differentiation / negative regulation of Notch signaling pathway / cholesterol biosynthetic process / endodermal cell differentiation / Activation of Matrix Metalloproteinases / metalloaminopeptidase activity / Collagen degradation / collagen catabolic process / endocytic vesicle / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of cholesterol efflux / extracellular matrix disassembly / regulation of protein localization to plasma membrane / Scavenging of heme from plasma / response to mechanical stimulus / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / Retinoid metabolism and transport / ovarian follicle development / positive regulation of stress fiber assembly / endocytic vesicle lumen / heat shock protein binding / Degradation of the extracellular matrix / cholesterol metabolic process / extracellular matrix organization / extracellular matrix / skeletal system development / cholesterol homeostasis Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / molecular dynamics | |||||||||
Authors | Marcink, T.C. / Van Doren, S.R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cm1.cif.gz | 10.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6cm1.ent.gz | 8.6 MB | Display | PDB format |
PDBx/mmJSON format | 6cm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/6cm1 ftp://data.pdbj.org/pub/pdb/validation_reports/cm/6cm1 | HTTPS FTP |
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-Related structure data
Related structure data | 6clzC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 | ||||||
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#2: Protein | 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 / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-CL / | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 20 mM Tri-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 the HPX domain to the nanodisc. NMR shaped tubes were used to obtain a better spectra Label: 2H, 13C, 15N / Solvent system: 93% H2O/7% D2O | ||||||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Details: MT1-MMP hemopexin-like domain along with the MSP1D1 and PX4 complex were suspended in a buffer containing 300 mM NaCl, 0.02% sodium azide, 93% water, 7% D2O, and 20 mM Tris pH 7.2 Ionic strength: 300 mM / Label: NMR Buffer / pH: 7.2 / Pressure: 1 atm / Temperature: 303 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 4 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 15 / Conformers submitted total number: 15 |