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- PDB-2n8r: Productive complex between MMP-12 and synthetic triple-helical co... -

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Basic information

Entry
Database: PDB / ID: 2n8r
TitleProductive complex between MMP-12 and synthetic triple-helical collagen, revealed through paramagnetic NMR
Components
  • Collagen triple helix repeat family protein
  • Macrophage metalloelastase
KeywordsHYDROLASE/STRUCTURAL PROTEIN / Collagenolysis / matrix petalloproteinase / HYDROLASE-STRUCTURAL PROTEIN complex
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 / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / 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
Macrophage metalloelastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Rigid-body docking, Conformer selection
Model detailsfewest violations, model1
AuthorsPrior, S.H. / Van Doren, S.R.
Citation
Journal: J.Biol.Chem. / Year: 2016
Title: Path to Collagenolysis: COLLAGEN V TRIPLE-HELIX MODEL BOUND PRODUCTIVELY AND IN ENCOUNTERS BY MATRIX METALLOPROTEINASE-12.
Authors: Prior, S.H. / Byrne, T.S. / Tokmina-Roszyk, D. / Fields, G.B. / Van Doren, S.R.
#1: Journal: J.Biomol.Nmr / Year: 2006
Title: 1H, 13C, and 15N peak assignments and secondary structure of human macrophage metalloelastase (MMP-12) in its inhibitor-free state.
Authors: Bhaskaran, R. / Van Doren, S.R.
History
DepositionOct 24, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Apr 27, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage metalloelastase
B: Collagen triple helix repeat family protein
C: Collagen triple helix repeat family protein
D: Collagen triple helix repeat family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3619
Polymers28,1104
Non-polymers2515
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 7500back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1fewest violations

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Components

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


Mass: 18235.410 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 / Keywords: MMP-12 / References: UniProt: P39900, macrophage elastase
#2: Protein/peptide Collagen triple helix repeat family protein


Mass: 3291.448 Da / Num. of mol.: 3 / Source method: obtained synthetically
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1322D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-99% 15N] MMP, 0.6 mM TOAC labelled in P5 position THP, 90% H2O/10% D2O90% H2O/10% D2O
20.25 mM [U-100% 12C; U-100% 15N; U-100% 2H; U-100% 13CH3] MMP, 0.38 mM TOAC labelled in P8' position THP, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMMMP-12-1[U-99% 15N]1
0.6 mMTHP-2TOAC labelled in P5 position1
0.25 mMMMP-12-3[U-100% 12C; U-100% 15N; U-100% 2H; U-100% 13CH3]2
0.38 mMTHP-4TOAC labelled in P8' position2
Sample conditionspH: 6.6 / Pressure: ambient / Temperature: 299 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TOPSPINBruker Biospincollection
TOPSPINBruker Biospinprocessing
AnalysisCCPNchemical shift assignment
AnalysisCCPNpeak picking
HADDOCK2.1Alexandre Bonvinstructure solution
q_test.pyStephen H. Priorstructure solution
GROMOSvan Gunsteren and Berendsenrefinement
HADDOCK2.1Alexandre Bonvinrefinement
q_test.pyStephen H. Priorrefinement
RefinementMethod: Rigid-body docking, Conformer selection / Software ordinal: 1
Details: The Collagen triple helix repeat peptide chain is homology-modeled from 4AUO. The Macrophage metalloelastase enzyme starting structure is 2poj.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 7500 / Conformers submitted total number: 1

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