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- PDB-2mcn: Distinct ubiquitin binding modes exhibited by SH3 domains: molecu... -

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Basic information

Entry
Database: PDB / ID: 2mcn
TitleDistinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications
Components
  • CD2-associated protein
  • Ubiquitin
KeywordsCELL CYCLE/SIGNALING PROTEIN / CELL CYCLE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


neurotrophin signaling pathway / response to glial cell derived neurotrophic factor / transforming growth factor beta1 production / negative regulation of small GTPase mediated signal transduction / localization of cell / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / slit diaphragm / response to transforming growth factor beta / podocyte differentiation ...neurotrophin signaling pathway / response to glial cell derived neurotrophic factor / transforming growth factor beta1 production / negative regulation of small GTPase mediated signal transduction / localization of cell / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / slit diaphragm / response to transforming growth factor beta / podocyte differentiation / immunological synapse formation / endothelium development / nerve growth factor signaling pathway / protein heterooligomerization / collateral sprouting / renal albumin absorption / phosphatidylinositol 3-kinase regulatory subunit binding / cell-cell adhesion mediated by cadherin / glomerulus development / filopodium assembly / membrane organization / cell-cell junction organization / podosome / clathrin binding / maintenance of blood-brain barrier / nuclear envelope lumen / D-glucose import / filamentous actin / neurotrophin TRK receptor signaling pathway / protein secretion / adipose tissue development / lymph node development / stress-activated MAPK cascade / ruffle / Maturation of protein E / Maturation of protein E / actin filament polymerization / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / ERK1 and ERK2 cascade / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / liver development / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / actin filament organization / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / trans-Golgi network membrane / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / TNFR1-induced NF-kappa-B signaling pathway / cell periphery / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin
Similarity search - Function
CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / : / Variant SH3 domain / SH3 Domains / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SH3 domain / Src homology 3 domains / SH3 type barrels. ...CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / : / Variant SH3 domain / SH3 Domains / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SH3 domain / Src homology 3 domains / SH3 type barrels. / : / SH3-like domain superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Src homology 3 (SH3) domain profile. / SH3 domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / CD2-associated protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, docking, simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsOrtega-Roldan, J. / Salmon, L. / Azuaga, A. / Blackledge, M. / Van Nuland, N.
CitationJournal: 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
DepositionAug 22, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD2-associated protein
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)15,8582
Polymers15,8582
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)10 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein CD2-associated protein / Mesenchyme-to-epithelium transition protein with SH3 domains 1 / METS-1


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
#2: Protein Ubiquitin


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1233D HNCO JNH, JCC, JCH, JCAHA
1343D HNCO JNH, JCC, JCH, JCAHA
1453D HNCO JNH, JCC, JCH, JCAHA
1562D 1H-15N HSQC FILTERED DIPSAP
1622D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM [U-99% 15N] CD2AP SH3-A, 1 mM ubiquitin, 90% H2O/10% D2O90% H2O/10% D2O
20.25 mM [U-99% 15N] ubiquitin, mM CD2AP SH3-A, 90% H2O/10% D2O90% H2O/10% D2O
30.9 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 0.46 mM [U-99% 15N ubiquitin90% H2O/10% D2O
40.8 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 1.37 mM [U-99% 15N] ubiquitin90% H2O/10% D2O
50.7 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 1.75 mM [U-99% 15N] ubiquitin90% H2O/10% D2O
60.25 mM [U-99% 13C; U-99% 15N] CD2AP SH3-A, 1.75 MM [U-99% 15N] ubiquitin90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Uniform NMR SystemVarianUniform NMR System6001
Varian Uniform NMR SystemVarianUniform NMR System8002

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Processing

NMR software
NameDeveloperClassification
HADDOCKDominguez, Boelensrefinement
CNS/SCULPTORBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRViewJohnson, One Moon Scientificstructure solution
HADDOCKBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS/SCULPTORrefinement
HADDOCKBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, molecular dynamics, docking, simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 10

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