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- PDB-2d9s: Solution structure of RSGI RUH-049, a UBA domain from mouse cDNA -

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Basic information

Entry
Database: PDB / ID: 2d9s
TitleSolution structure of RSGI RUH-049, a UBA domain from mouse cDNA
ComponentsCBL E3 ubiquitin protein ligase
KeywordsLIGASE / UBA domain / dimer / protein binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / TGF-beta receptor signaling activates SMADs / mast cell granule / Regulation of KIT signaling / Interleukin-6 signaling / : / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling ...: / TGF-beta receptor signaling activates SMADs / mast cell granule / Regulation of KIT signaling / Interleukin-6 signaling / : / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / : / Spry regulation of FGF signaling / Negative regulation of MET activity / negative regulation of epidermal growth factor-activated receptor activity / EGFR downregulation / regulation of platelet-derived growth factor receptor-alpha signaling pathway / cellular response to oxygen-glucose deprivation / regulation of Rap protein signal transduction / Regulation of signaling by CBL / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / phosphatidylinositol 3-kinase regulatory subunit binding / epidermal growth factor receptor binding / mast cell degranulation / response to testosterone / cellular response to platelet-derived growth factor stimulus / negative regulation of epidermal growth factor receptor signaling pathway / response to starvation / protein monoubiquitination / bone resorption / cellular response to epidermal growth factor stimulus / phosphotyrosine residue binding / ephrin receptor binding / protein tyrosine kinase binding / cellular response to nerve growth factor stimulus / response to activity / response to gamma radiation / RING-type E3 ubiquitin transferase / cilium / receptor tyrosine kinase binding / SH3 domain binding / positive regulation of receptor-mediated endocytosis / protein polyubiquitination / male gonad development / ubiquitin protein ligase activity / growth cone / ubiquitin-dependent protein catabolic process / response to ethanol / cell surface receptor signaling pathway / membrane raft / axon / protein phosphorylation / response to antibiotic / focal adhesion / DNA damage response / calcium ion binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / plasma membrane / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. ...E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / Adaptor protein Cbl, N-terminal domain superfamily / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CBL
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHamada, T. / Hirota, H. / Lin, Y.-J. / Guntert, P. / Kurosaki, C. / Izumi, K. / Yoshida, M. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of RSGI RUH-049, a UBA domain from mouse cDNA
Authors: Hamada, T. / Lin, Y.-J. / Kurosaki, C. / Koshiba, S. / Inoue, M. / Kigawa, T. / Hayashi, F. / Muto, Y. / Izumi, K. / Yoshida, M. / Akasaka, R. / Kukimoto, M. / Terada, T. / Shirouzu, M. / ...Authors: Hamada, T. / Lin, Y.-J. / Kurosaki, C. / Koshiba, S. / Inoue, M. / Kigawa, T. / Hayashi, F. / Muto, Y. / Izumi, K. / Yoshida, M. / Akasaka, R. / Kukimoto, M. / Terada, T. / Shirouzu, M. / Tanaka, A. / Hayashizaki, Y. / Guntert, P. / Yokoyama, S. / Hirota, H.
History
DepositionDec 13, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBL E3 ubiquitin protein ligase
B: CBL E3 ubiquitin protein ligase


Theoretical massNumber of molelcules
Total (without water)11,3592
Polymers11,3592
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)20 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein CBL E3 ubiquitin protein ligase / Signal transduction protein CBL / Proto-oncogene c-CBL / Casitas B-lineage lymphoma proto- oncogene


Mass: 5679.253 Da / Num. of mol.: 2 / Fragment: UBA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: Cbl / Plasmid: P041108-06
References: UniProt: P22682, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1323D 13C F1-filtered F3-edited NOESY
NMR detailsText: This structure was determined using 3D NMR techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM UBA domain U-15N, 13C; 20mM d-Tris-HCl buffer (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN390% H2O/10% D2O
21.2mM UBA domain U-15N, 13C; 1.2mM UBA domain; 20mM d-Tris-HCl buffer (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3100% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
JEOL ECAJEOLECA7001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
Delta NMR4.3JEOLcollection
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.9295Kobayashi, N.data analysis
CYANA2.2.1Guntert, P. et al.structure solution
OPALp1.4Koradi, R., Billeter, M., Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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