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- PDB-2lz6: Distinct ubiquitin binding modes exhibited by sh3 domains: molecu... -

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Basic information

Entry
Database: PDB / ID: 2lz6
TitleDistinct ubiquitin binding modes exhibited by sh3 domains: molecular determinants and functional implications
Components
  • CD2-associated protein
  • Ubiquitin
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


regulation of receptor-mediated endocytosis / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / vascular endothelial growth factor receptor binding / negative regulation of transforming growth factor beta1 production / response to transforming growth factor beta / vesicle organization / immunological synapse formation / protein heterooligomerization / podosome ...regulation of receptor-mediated endocytosis / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / vascular endothelial growth factor receptor binding / negative regulation of transforming growth factor beta1 production / response to transforming growth factor beta / vesicle organization / immunological synapse formation / protein heterooligomerization / podosome / cell leading edge / filamentous actin / endocytic vesicle / centriolar satellite / 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 / 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 / ruffle / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / APC/C:Cdc20 mediated degradation of Securin / kidney development / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / actin filament organization / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / actin filament / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / cell periphery / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / positive regulation of protein secretion / Hh mutants are degraded by ERAD / regulation of actin cytoskeleton organization
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 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. ...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 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Src homology 3 domains / SH3 type barrels. / Ubiquitin-like (UB roll) / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / CD2-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodSOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS
Model detailslowest energy, model 1
AuthorsOrtega-Roldan, J. / 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
DepositionSep 24, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: 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 ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: CD2-associated protein


Theoretical massNumber of molelcules
Total (without water)15,7242
Polymers15,7242
Non-polymers00
Water0
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 Ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0CG48
#2: Protein CD2-associated protein / Mesenchyme-to-epithelium transition protein with SH3 domains 1 / METS-1


Mass: 7146.910 Da / Num. of mol.: 1 / Fragment: SH3 3 DOMAIN RESIDUES 270-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd2ap, Mets1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9JLQ0

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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-C, 1 mM Ubiquitin, 90% H2O/10% D2O90% H2O/10% D2O
20.25 mM [U-99% 15N] Ubiquitin, 1 mM CD2AP SH3-C, 90% H2O/10% D2O90% H2O/10% D2O
30.9 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 0.46 mM [U-99% 15N] Ubiquitin, 90% H2O/10% D2O90% H2O/10% D2O
40.828 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.37 mM [U-99% 15N] Ubiquitin, 90% H2O/10% D2O90% H2O/10% D2O
50.78 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.75 mM [U-99% 15N] Ubiquitin, 90% H2O/10% D2O90% H2O/10% D2O
60.25 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.75 mM [U-99% 15N] Ubiquitin, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMCD2AP SH3-C-1[U-99% 15N]1
1 mMUbiquitin-21
0.25 mMUbiquitin-3[U-99% 15N]2
1 mMCD2AP SH3-C-42
0.9 mMCD2AP SH3-C-5[U-99% 13C; U-99% 15N]3
0.46 mMUbiquitin-6[U-99% 15N]3
0.828 mMCD2AP SH3-C-7[U-99% 13C; U-99% 15N]4
1.37 mMUbiquitin-8[U-99% 15N]4
0.78 mMCD2AP SH3-C-9[U-99% 13C; U-99% 15N]5
1.75 mMUbiquitin-10[U-99% 15N]5
0.25 mMCD2AP SH3-C-11[U-99% 13C; U-99% 15N]6
1.75 mMUbiquitin-12[U-99% 15N]6
Sample conditionsIonic strength: 0 / pH: 6.0 / 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
HADDOCKAlexandre Bonvinrefinement
CNS/SCULPTORBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS/SCULPTORBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRViewJohnson, One Moon Scientificstructure solution
HADDOCKAlexandre Bonvinstructure solution
RefinementMethod: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1 / Details: DOCKING
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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