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- PDB-2mlr: Membrane Bilayer complex with Matrix Metalloproteinase-12 at its ... -

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Basic information

Entry
Database: PDB / ID: 2mlr
TitleMembrane Bilayer complex with Matrix Metalloproteinase-12 at its Alpha-face
ComponentsMacrophage metalloelastase
KeywordsHYDROLASE / Membrane-binding of soluble metalloproteinase MMP-12 / Catalytic domain
Function / homology
Function and homology information


macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development ...macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development / positive regulation of interferon-alpha production / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / core promoter sequence-specific DNA binding / collagen binding / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / cellular response to virus / protein import into nucleus / endopeptidase activity / sequence-specific DNA binding / serine-type endopeptidase activity / calcium ion binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm
Similarity search - Function
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 ...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. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Macrophage metalloelastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsKoppisetti, R.K. / Fulcher, Y.G. / Prior, S.H. / Lenoir, M. / Overduin, M. / Van Doren, S.R.
CitationJournal: Nat Commun / Year: 2014
Title: Ambidextrous binding of cell and membrane bilayers by soluble matrix metalloproteinase-12.
Authors: Koppisetti, R.K. / Fulcher, Y.G. / Jurkevich, A. / Prior, S.H. / Xu, J. / Lenoir, M. / Overduin, M. / Van Doren, S.R.
History
DepositionMar 4, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,296131
Polymers18,1771
Non-polymers85,119130
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 14structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Macrophage metalloelastase / MME / Macrophage elastase / ME / hME / Matrix metalloproteinase-12 / MMP-12


Mass: 18177.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP12, HME / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P39900, macrophage elastase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical...
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine


Mass: 678.940 Da / Num. of mol.: 125 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: MMP-12 bound with its Alpha-face toward DMPC bilayer at its proximity leaflet.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
232NMR relaxation experiments
NMR detailsText: NMR relaxation experiments(PRE based)

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] Matrix Metalloproteinase-12, 90% H2O/10% D2O90% H2O/10% D2O
280 mM na DMPC/DHPC(1:2), 20mM Tris20mM Tris
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMatrix Metalloproteinase-12-1[U-100% 13C; U-100% 15N]1
80 mMDMPC/DHPC(1:2)-2na2
Sample conditions
Conditions-IDIonic strengthpHPressure unitsTemperature (K)
1and 20uM ZnCl2 6.6 atm300 K
220mM Tris 7.0 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance II / Manufacturer: Bruker / Model: Avance II / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
SPARKYGoddarddata analysis
GROMACSBERENDSENrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Temperature equilibration(NVT) for 200ps and NPT(pressure) equilibration for 1ns followed by production MD 15ns.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 14 / Conformers submitted total number: 14

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