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- PDB-3buw: Crystal structure of c-Cbl-TKB domain complexed with its binding ... -

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Basic information

Entry
Database: PDB / ID: 3buw
TitleCrystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk
Components
  • 13-meric peptide from Tyrosine-protein kinase SYK
  • E3 ubiquitin-protein ligase CBL
KeywordsLIGASE/SIGNALING PROTEIN / Cbl / TKB / ligase / signal transduction / proto-oncogene / complex / Alternative splicing / ATP-binding / Host-virus interaction / Kinase / Nucleotide-binding / Phosphoprotein / Polymorphism / SH2 domain / Transferase / Tyrosine-protein kinase / Ubl conjugation / Calcium / Cytoplasm / Metal-binding / Ubl conjugation pathway / Zinc / Zinc-finger / LIGASE-SIGNALING PROTEIN COMPLEX
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 / interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / positive regulation of interleukin-3 production / cellular response to lectin / B cell receptor complex ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / positive regulation of interleukin-3 production / cellular response to lectin / B cell receptor complex / Toll-like receptor binding / regulation of platelet aggregation / positive regulation of alpha-beta T cell proliferation / serotonin secretion by platelet / leukocyte activation involved in immune response / neutrophil activation involved in immune response / lymph vessel development / positive regulation of mast cell degranulation / gamma-delta T cell differentiation / positive regulation of mast cell cytokine production / collagen-activated tyrosine kinase receptor signaling pathway / positive regulation of gamma-delta T cell differentiation / cell surface pattern recognition receptor signaling pathway / regulation of platelet activation / cell activation / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / beta selection / cellular response to molecule of fungal origin / FLT3 signaling through SRC family kinases / early phagosome / leukotriene biosynthetic process / regulation of phagocytosis / regulation of DNA-binding transcription factor activity / regulation of tumor necrosis factor-mediated signaling pathway / macrophage activation involved in immune response / interleukin-3-mediated signaling pathway / positive regulation of bone resorption / positive regulation of monocyte chemotactic protein-1 production / cellular response to lipid / Fc epsilon receptor (FCERI) signaling / Interleukin-2 signaling / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of alpha-beta T cell differentiation / blood vessel morphogenesis / positive regulation of cell adhesion mediated by integrin / Regulation of KIT signaling / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of B cell differentiation / T cell receptor complex / leukocyte cell-cell adhesion / Interleukin-6 signaling / mast cell degranulation / response to starvation / Dectin-2 family / response to testosterone / positive regulation of interleukin-4 production / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of epidermal growth factor receptor signaling pathway / amyloid-beta clearance / TGF-beta receptor signaling activates SMADs / positive regulation of interleukin-10 production / positive regulation of receptor internalization / FCGR activation / cellular response to low-density lipoprotein particle stimulus / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of type I interferon production / protein monoubiquitination / Role of phospholipids in phagocytosis / phosphatase binding / regulation of ERK1 and ERK2 cascade / protein autoubiquitination / phospholipase binding / GPVI-mediated activation cascade / ephrin receptor binding / Signaling by CSF3 (G-CSF) / positive regulation of superoxide anion generation / cellular response to platelet-derived growth factor stimulus / phosphotyrosine residue binding / neutrophil chemotaxis / Integrin signaling / positive regulation of interleukin-12 production / FLT3 signaling by CBL mutants / positive regulation of TORC1 signaling / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / FCERI mediated Ca+2 mobilization / SH2 domain binding / positive regulation of calcium-mediated signaling / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / peptidyl-tyrosine phosphorylation / InlB-mediated entry of Listeria monocytogenes into host cell / B cell differentiation / animal organ morphogenesis / response to activity / response to gamma radiation / integrin-mediated signaling pathway
Similarity search - Function
Adaptor protein Cbl, N-terminal domain / 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 / 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 / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / Transcription Elongation Factor S-II; Chain A / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / SH2 domain / SHC Adaptor Protein / UBA-like superfamily / : / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Ring finger / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Zinc finger RING-type profile. / SH2 domain / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Zinc finger, RING/FYVE/PHD-type / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CBL / Tyrosine-protein kinase SYK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsNg, C. / Jackson, R.A. / Buschdorf, J.P. / Sun, Q. / Guy, G.R. / Sivaraman, J.
CitationJournal: Embo J. / Year: 2008
Title: Structural basis for a novel intrapeptidyl H-bond and reverse binding of c-Cbl-TKB domain substrates
Authors: Ng, C. / Jackson, R.A. / Buschdorf, J.P. / Sun, Q. / Guy, G.R. / Sivaraman, J.
History
DepositionJan 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 13-meric peptide from Tyrosine-protein kinase SYK
B: E3 ubiquitin-protein ligase CBL
C: 13-meric peptide from Tyrosine-protein kinase SYK
D: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)79,4714
Polymers79,4714
Non-polymers00
Water10,359575
1
A: 13-meric peptide from Tyrosine-protein kinase SYK


Theoretical massNumber of molelcules
Total (without water)1,5441
Polymers1,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)38,1921
Polymers38,1921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 13-meric peptide from Tyrosine-protein kinase SYK


Theoretical massNumber of molelcules
Total (without water)1,5441
Polymers1,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)38,1921
Polymers38,1921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: 13-meric peptide from Tyrosine-protein kinase SYK
B: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)39,7362
Polymers39,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-8.8 kcal/mol
Surface area15210 Å2
MethodPISA
6
C: 13-meric peptide from Tyrosine-protein kinase SYK
D: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)39,7362
Polymers39,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-8.7 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.793, 104.809, 52.778
Angle α, β, γ (deg.)90.000, 89.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide 13-meric peptide from Tyrosine-protein kinase SYK / Spleen tyrosine kinase


Mass: 1543.565 Da / Num. of mol.: 2 / Fragment: UNP residues 317-329, pTyr-323 phosphopeptide / Source method: obtained synthetically / Details: synthetic construct / References: UniProt: P43405
#2: Protein E3 ubiquitin-protein ligase CBL / Signal transduction protein CBL / Proto-oncogene c-CBL / Casitas B-lineage lymphoma proto-oncogene ...Signal transduction protein CBL / Proto-oncogene c-CBL / Casitas B-lineage lymphoma proto-oncogene / RING finger protein 55


Mass: 38192.090 Da / Num. of mol.: 2
Fragment: c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55
Plasmid details: Cas-Br-M (murine) ecotropic retroviral transforming sequence
Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.12M ammonium acetate, 18% PEG 3350, pH 6.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→40 Å / Num. obs: 113559 / % possible obs: 92.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.075 / Χ2: 0.767 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.45-1.53.30.25480580.3366
1.5-1.563.80.22594290.37677.2
1.56-1.634.40.213108360.40588.7
1.63-1.725.10.193118160.43496.7
1.72-1.835.80.163121460.48599.1
1.83-1.976.20.123121680.60599.5
1.97-2.176.70.092122150.86899.8
2.17-2.486.90.085122741.11799.9
2.48-3.1270.07122751.10999.9
3.12-407.30.063123420.98599.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CBL

2cbl


Resolution: 1.45→20 Å / Cross valid method: THROUGHOUT / σ(F): 15493
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2176 1.8 %RANDOM
Rwork0.224 ---
obs-97683 79.8 %-
Solvent computationBsol: 46.214 Å2
Displacement parametersBiso mean: 23.012 Å2
Baniso -1Baniso -2Baniso -3
1--4.824 Å20 Å20.151 Å2
2--2.555 Å20 Å2
3---2.269 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5156 0 0 575 5731
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.103
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ptr.param

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