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- PDB-2m2f: The membran-proximal domain of ADAM17 -

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Basic information

Entry
Database: PDB / ID: 2m2f
TitleThe membran-proximal domain of ADAM17
ComponentsDisintegrin and metalloproteinase domain-containing protein 17
KeywordsHYDROLASE REGULATOR / ADAM17 / Membrane-proximal domain / Closed conformer
Function / homology
Function and homology information


ADAM 17 endopeptidase / regulation of mast cell apoptotic process / positive regulation of epidermal growth factor-activated receptor activity / signal release / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / cellular response to high density lipoprotein particle stimulus / production of molecular mediator involved in inflammatory response / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / Notch receptor processing / interleukin-6 receptor binding ...ADAM 17 endopeptidase / regulation of mast cell apoptotic process / positive regulation of epidermal growth factor-activated receptor activity / signal release / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / cellular response to high density lipoprotein particle stimulus / production of molecular mediator involved in inflammatory response / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / Notch receptor processing / interleukin-6 receptor binding / tumor necrosis factor binding / positive regulation of T cell chemotaxis / TNF signaling / cytokine precursor processing / regulation of axon regeneration / positive regulation of leukocyte chemotaxis / metallodipeptidase activity / Release of Hh-Np from the secreting cell / Regulated proteolysis of p75NTR / commissural neuron axon guidance / regulation of neuron migration / positive regulation of tumor necrosis factor-mediated signaling pathway / neutrophil mediated immunity / germinal center formation / Notch binding / wound healing, spreading of epidermal cells / positive regulation of vascular endothelial cell proliferation / negative regulation of cold-induced thermogenesis / CD163 mediating an anti-inflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / cell adhesion mediated by integrin / Signaling by EGFR / amyloid precursor protein catabolic process / cytokine binding / Collagen degradation / membrane protein ectodomain proteolysis / positive regulation of blood vessel endothelial cell migration / positive regulation of G1/S transition of mitotic cell cycle / Growth hormone receptor signaling / Nuclear signaling by ERBB4 / positive regulation of chemokine production / spleen development / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / B cell differentiation / Activated NOTCH1 Transmits Signal to the Nucleus / PDZ domain binding / cell motility / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transforming growth factor beta receptor signaling pathway / metalloendopeptidase activity / protein processing / SH3 domain binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / epidermal growth factor receptor signaling pathway / metallopeptidase activity / positive regulation of tumor necrosis factor production / integrin binding / T cell differentiation in thymus / peptidase activity / actin cytoskeleton / negative regulation of neuron projection development / positive regulation of cell growth / endopeptidase activity / response to lipopolysaccharide / response to hypoxia / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / apical plasma membrane / membrane raft / response to xenobiotic stimulus / endoplasmic reticulum lumen / Golgi membrane / positive regulation of cell population proliferation / cell surface / proteolysis / metal ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Echistatin - #30 / Echistatin / ADAM17, membrane-proximal domain / Membrane-proximal domain, switch, for ADAM17 / Metallo-peptidase family M12 / ADAM10/ADAM17 catalytic domain / : / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins ...Echistatin - #30 / Echistatin / ADAM17, membrane-proximal domain / Membrane-proximal domain, switch, for ADAM17 / Metallo-peptidase family M12 / ADAM10/ADAM17 catalytic domain / : / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Disintegrin and metalloproteinase domain-containing protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsDuesterhoeft, S. / Jung, S. / Hung, C. / Tholey, A. / Soennichsen, F.D. / Groetzinger, J. / Lorenzen, I.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Membrane-proximal domain of a disintegrin and metalloprotease-17 represents the putative molecular switch of its shedding activity operated by protein-disulfide isomerase.
Authors: Dusterhoft, S. / Jung, S. / Hung, C.W. / Tholey, A. / Sonnichsen, F.D. / Grotzinger, J. / Lorenzen, I.
History
DepositionDec 20, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disintegrin and metalloproteinase domain-containing protein 17


Theoretical massNumber of molelcules
Total (without water)9,9051
Polymers9,9051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Disintegrin and metalloproteinase domain-containing protein 17 / ADAM 17 / Snake venom-like protease / TNF-alpha convertase / TNF-alpha-converting enzyme


Mass: 9905.123 Da / Num. of mol.: 1 / Fragment: UNP residues 581-642
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAM17, CSVP, TACE / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: P78536, ADAM 17 endopeptidase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Memnbran proximal domain of ADAM17
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HNCO
1413D HN(CO)CA
1513D H(CCO)NH
1613D HN(CA)CO
1713D HN(CO)CA
1813D CBCA(CO)NH
1913D HN(CA)CB
11013D 1H-15N NOESY
11113D 1H-15N TOCSY
11213D 1H-13C NOESY
11313D 1H-13C NOESY aliphatic

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Sample preparation

DetailsContents: 1.0 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: entity-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.15 / pH: 7.4 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Bruker Avance 600 / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeJohnson, One Moon Scientificprocessing
NMRPipeJohnson, One Moon Scientificdata analysis
CYANArefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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