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- PDB-2k6d: CIN85 Sh3-C domain in complex with ubiquitin -

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Basic information

Entry
Database: PDB / ID: 2k6d
TitleCIN85 Sh3-C domain in complex with ubiquitin
Components
  • SH3 domain-containing kinase-binding protein 1
  • Ubiquitin
KeywordsSH3 DOMAIN/UBIQUITIN / CIN85 / SH3 domain / ubiquitin / Alternative splicing / Apoptosis / Cell junction / Coiled coil / Cytoplasm / Cytoplasmic vesicle / Cytoskeleton / Endocytosis / Membrane / Phosphoprotein / Polymorphism / SH3-binding / Synapse / Synaptosome / Ubl conjugation / Nucleus / SH3 DOMAIN-UBIQUITIN COMPLEX
Function / homology
Function and homology information


: / : / protein modification process => GO:0036211 / Reelin signalling pathway / positive regulation of B cell activation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / endocytic vesicle ...: / : / protein modification process => GO:0036211 / Reelin signalling pathway / positive regulation of B cell activation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / endocytic vesicle / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Maturation of protein E / Maturation of protein E / cytoskeleton organization / cytosolic ribosome / 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 / 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 / cytoplasmic vesicle membrane / 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 / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / 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 / 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 / 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) / TNFR1-induced NF-kappa-B signaling pathway / GABA-ergic synapse / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL
Similarity search - Function
SH3 domain-containing kinase-binding protein 1, first SH3 domain / SH3 domain-containing kinase-binding protein 1, second SH3 domain / SH3 domain-containing kinase-binding protein 1, third SH3 domain / : / Variant SH3 domain / SH3 Domains / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily ...SH3 domain-containing kinase-binding protein 1, first SH3 domain / SH3 domain-containing kinase-binding protein 1, second SH3 domain / SH3 domain-containing kinase-binding protein 1, third SH3 domain / : / Variant SH3 domain / SH3 Domains / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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 / Ubiquitin-60S ribosomal protein L40 / SH3 domain-containing kinase-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsForman-Kay, J. / Bezsonova, I.
CitationJournal: Biochemistry / Year: 2008
Title: Interactions between the three CIN85 SH3 domains and ubiquitin: implications for CIN85 ubiquitination.
Authors: Bezsonova, I. / Bruce, M.C. / Wiesner, S. / Lin, H. / Rotin, D. / Forman-Kay, J.D.
History
DepositionJul 7, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 4, 2018Group: Data collection / Derived calculations / Experimental preparation
Category: pdbx_nmr_sample_details / pdbx_struct_assembly ...pdbx_nmr_sample_details / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _pdbx_nmr_sample_details.contents
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH3 domain-containing kinase-binding protein 1
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)15,7742
Polymers15,7742
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein SH3 domain-containing kinase-binding protein 1 / Cbl-interacting protein of 85 kDa / Human Src family kinase-binding protein 1 / HSB-1 / CD2-binding ...Cbl-interacting protein of 85 kDa / Human Src family kinase-binding protein 1 / HSB-1 / CD2-binding protein 3 / CD2BP3


Mass: 7151.092 Da / Num. of mol.: 1 / Fragment: CIN85 SH3-C domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SH3KBP1, CIN85 / Plasmid: pET28-b / Production host: Escherichia coli (E. coli) / References: UniProt: Q96B97
#2: Protein Ubiquitin


Mass: 8622.922 Da / Num. of mol.: 1 / Fragment: ubiquitin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62988, UniProt: P0CG48*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-15N HSQC
1333D HN(CA)CB
142IPAP
151IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
10.1 mM CIN85, 0.1 mM [U-100% 15N] ubiquitin, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.1 mM [U-100% 15N] CIN85, 0.1 mM ubiquitiny, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N] CIN85, 50 mM sodium phosphate, 2 mM DTT, 5 mM DSS, 150 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mMCIN851
0.1 mMubiquitin[U-100% 15N]1
50 mMsodium phosphate1
2 mMDTT1
5 mMDSS1
150 mMsodium chloride1
0.1 mMCIN85[U-100% 15N]2
0.1 mMubiquitiny2
50 mMsodium phosphate2
2 mMDTT2
5 mMDSS2
150 mMsodium chloride2
1.0 mMCIN85[U-100% 13C; U-100% 15N]3
50 mMsodium phosphate3
2 mMDTT3
5 mMDSS3
150 mMsodium chloride3
Sample conditionsIonic strength: 0.15 / pH: 6.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
HADDOCKCyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvinstructure solution
HADDOCKCyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 8

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