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Yorodumi- PDB-2mcn: Distinct ubiquitin binding modes exhibited by SH3 domains: molecu... -
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-Basic information
Entry | Database: PDB / ID: 2mcn | ||||||
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Title | Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications | ||||||
Components |
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Keywords | CELL CYCLE/SIGNALING PROTEIN / CELL CYCLE-SIGNALING PROTEIN complex | ||||||
Function / homology | Function and homology information neurotrophin signaling pathway / response to glial cell derived neurotrophic factor / regulation of receptor-mediated endocytosis / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / localization of cell / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / vascular endothelial growth factor receptor binding / slit diaphragm ...neurotrophin signaling pathway / response to glial cell derived neurotrophic factor / regulation of receptor-mediated endocytosis / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / localization of cell / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / vascular endothelial growth factor receptor binding / slit diaphragm / response to transforming growth factor beta / podocyte differentiation / vesicle organization / immunological synapse formation / endothelium development / nerve growth factor signaling pathway / cell-cell adhesion mediated by cadherin / collateral sprouting / protein heterooligomerization / renal albumin absorption / phosphatidylinositol 3-kinase regulatory subunit binding / glomerulus development / membrane organization / filopodium assembly / cell-cell junction organization / podosome / clathrin binding / maintenance of blood-brain barrier / nuclear envelope lumen / glucose import / cell leading edge / filamentous actin / neurotrophin TRK receptor signaling pathway / endocytic vesicle / centriolar satellite / protein secretion / lymph node development / adipose tissue development / stress-activated MAPK cascade / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / ruffle / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / ERK1 and ERK2 cascade / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / actin filament polymerization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics, docking, simulated annealing, molecular dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Ortega-Roldan, J. / Salmon, L. / Azuaga, A. / Blackledge, M. / Van Nuland, N. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications. Authors: Ortega Roldan, J.L. / Casares, S. / Ringkjbing Jensen, M. / Cardenes, N. / Bravo, J. / Blackledge, M. / Azuaga, A.I. / van Nuland, N.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mcn.cif.gz | 424.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mcn.ent.gz | 352.9 KB | Display | PDB format |
PDBx/mmJSON format | 2mcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mcn_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 2mcn_full_validation.pdf.gz | 12.3 MB | Display | |
Data in XML | 2mcn_validation.xml.gz | 861.8 KB | Display | |
Data in CIF | 2mcn_validation.cif.gz | 935 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/2mcn ftp://data.pdbj.org/pub/pdb/validation_reports/mc/2mcn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7281.089 Da / Num. of mol.: 1 / Fragment: SH3A domain (UNP residues 2-58) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd2ap, Mets1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JLQ0 |
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#2: Protein | Mass: 8576.831 Da / Num. of mol.: 1 / Fragment: UNP residues 1-76 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: 0 / pH: 6 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics, docking, simulated annealing, molecular dynamics Software ordinal: 1 | |||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 10 |