- PDB-2n8r: Productive complex between MMP-12 and synthetic triple-helical co... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2n8r
Title
Productive complex between MMP-12 and synthetic triple-helical collagen, revealed through paramagnetic NMR
Components
Collagen triple helix repeat family protein
Macrophage metalloelastase
Keywords
HYDROLASE/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 / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / positive regulation of interferon-alpha production / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / cellular response to virus / metalloendopeptidase activity / 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
#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.
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
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
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D 1H-15N HSQC
1
2
2
2D 1H-15N HSQC
1
3
2
2D 1H-13C HSQC
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
0.4 mM [U-99% 15N] MMP, 0.6 mM TOAC labelled in P5 position THP, 90% H2O/10% D2O
90% H2O/10% D2O
2
0.25 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% D2O
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.4mM
MMP-12-1
[U-99% 15N]
1
0.6mM
THP-2
TOAClabelledinP5position
1
0.25mM
MMP-12-3
[U-100% 12C; U-100% 15N; U-100% 2H; U-100% 13CH3]
2
0.38mM
THP-4
TOAClabelledinP8' position
2
Sample conditions
pH: 6.6 / Pressure: ambient / Temperature: 299 K
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NMR measurement
NMR spectrometer
Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz
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Processing
NMR software
Name
Version
Developer
Classification
TOPSPIN
BrukerBiospin
collection
TOPSPIN
BrukerBiospin
processing
Analysis
CCPN
chemicalshiftassignment
Analysis
CCPN
peakpicking
HADDOCK
2.1
AlexandreBonvin
structuresolution
q_test.py
StephenH. Prior
structuresolution
GROMOS
vanGunsterenandBerendsen
refinement
HADDOCK
2.1
AlexandreBonvin
refinement
q_test.py
StephenH. Prior
refinement
Refinement
Method: 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 representative
Selection criteria: fewest violations
NMR ensemble
Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 7500 / Conformers submitted total number: 1
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