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- PDB-2juj: Solution Structure of the UBA domain from c-Cbl -

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Basic information

Entry
Database: PDB / ID: 2juj
TitleSolution Structure of the UBA domain from c-Cbl
ComponentsE3 ubiquitin-protein ligase CBL
KeywordsLIGASE / alpha helix / UBA domain / Calcium / Cytoplasm / Metal-binding / Phosphorylation / Proto-oncogene / SH2 domain / Ubl conjugation pathway / Zinc / Zinc-finger
Function / homology
Function and homology information


regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / entry of bacterium into host cell / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / entry of bacterium into host cell / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling / response to testosterone / negative regulation of epidermal growth factor receptor signaling pathway / cellular response to platelet-derived growth factor stimulus / response to starvation / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / protein autoubiquitination / FLT3 signaling by CBL mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / phosphotyrosine residue binding / ephrin receptor binding / InlB-mediated entry of Listeria monocytogenes into host cell / cellular response to nerve growth factor stimulus / response to activity / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / response to gamma radiation / Negative regulation of FGFR2 signaling / EGFR downregulation / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / Constitutive Signaling by EGFRvIII / RING-type E3 ubiquitin transferase / Negative regulation of MET activity / cilium / receptor tyrosine kinase binding / SH3 domain binding / protein polyubiquitination / cytokine-mediated signaling pathway / positive regulation of receptor-mediated endocytosis / ubiquitin-protein transferase activity / male gonad development / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin protein ligase activity / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / growth cone / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cadherin binding / membrane raft / focal adhesion / DNA damage response / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / plasma membrane / cytosol
Similarity search - Function
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 ...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 / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Helicase, Ruva Protein; domain 3 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CBL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsZhou, Z.R. / Hong, J. / Lin, D.H. / Hu, H.Y.
CitationJournal: Protein Sci. / Year: 2008
Title: Differential Ubiquitin Binding of the UBA Domains from Human c-Cbl and Cbl-b: NMR Structural and Biochemical Insights.
Authors: Zhou, Z.R. / Gao, H.C. / Zhou, C.J. / Chang, Y.G. / Hong, J. / Song, A.X. / Lin, D.H. / Hu, H.Y.
History
DepositionAug 30, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)6,1131
Polymers6,1131
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)15 / 20015 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein E3 ubiquitin-protein ligase CBL / c-Cbl / Signal transduction protein CBL / Proto-oncogene c-CBL / Casitas B-lineage lymphoma proto- ...c-Cbl / Signal transduction protein CBL / Proto-oncogene c-CBL / Casitas B-lineage lymphoma proto-oncogene / RING finger protein 55


Mass: 6112.852 Da / Num. of mol.: 1 / Fragment: UBA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P22681, 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
1122D 1H-15N HSQC
1223D HN(CA)CB
1323D CBCA(CO)NH
1423D HNCO
1513D HNHA
1633D (H)CCH-TOCSY
1713D 1H-15N NOESY
1833D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
120mM sodium phosphate, 50mM sodium chloride, 1mM DTT, 90% H2O, 10% D2O90% H2O/10% D2O
220mM sodium phosphate, 50mM sodium chloride, 1mM DTT, 90% H2O, 10% D2O90% H2O/10% D2O
320mM sodium phosphate, 50mM sodium chloride, 1mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMsodium phosphate1
50 mMsodium chloride1
1 mMDTT1
20 mMsodium phosphate2
50 mMsodium chloride2
1 mMDTT2
20 mMsodium phosphate3
50 mMsodium chloride3
1 mMDTT3
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures were calculated with ARIA/CNS using torsion angle dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 15 structures for lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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