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

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Basic information

Entry
Database: PDB / ID: 3bun
TitleCrystal structure of c-Cbl-TKB domain complexed with its binding motif in Sprouty4
Components
  • 13-meric peptide from Protein sprouty homolog 4
  • E3 ubiquitin-protein ligase CBL
KeywordsLIGASE/SIGNALING PROTEIN / Cbl / TKB / ligase / signal transduction / proto-oncogene / complex / Alternative splicing / Cytoplasm / Developmental protein / Membrane / Calcium / Metal-binding / Phosphoprotein / SH2 domain / 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 / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of fibroblast growth factor receptor signaling pathway / ubiquitin-dependent endocytosis / animal organ development / regulation of Rap protein signal transduction / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / negative regulation of Ras protein signal transduction / Regulation of KIT signaling ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of fibroblast growth factor receptor signaling pathway / ubiquitin-dependent endocytosis / animal organ development / regulation of Rap protein signal transduction / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / negative regulation of Ras protein signal transduction / Regulation of KIT signaling / positive regulation of epidermal growth factor receptor signaling pathway / Interleukin-6 signaling / mast cell degranulation / response to starvation / response to testosterone / negative regulation of epidermal growth factor receptor signaling pathway / protein kinase inhibitor activity / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / protein autoubiquitination / ephrin receptor binding / cellular response to platelet-derived growth factor stimulus / phosphotyrosine residue binding / FLT3 signaling by CBL mutants / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / cellular response to leukemia inhibitory factor / InlB-mediated entry of Listeria monocytogenes into host cell / response to activity / response to gamma radiation / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / EGFR downregulation / Spry regulation of FGF signaling / Negative regulation of MET activity / Constitutive Signaling by EGFRvIII / cellular response to nerve growth factor stimulus / receptor tyrosine kinase binding / RING-type E3 ubiquitin transferase / negative regulation of ERK1 and ERK2 cascade / positive regulation of receptor-mediated endocytosis / SH3 domain binding / ruffle membrane / male gonad development / protein polyubiquitination / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin-protein transferase activity / 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 / response to ethanol / cellular response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cilium / cadherin binding / membrane raft / focal adhesion / calcium ion binding / DNA damage response / symbiont entry into host cell / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / zinc ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) 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 ...: / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) 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 / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CBL / Protein sprouty homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 1.3Sep 16, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / pdbx_entity_src_syn ...entity / pdbx_entity_src_syn / struct / struct_conn / struct_ref_seq_dif
Item: _entity.pdbx_description / _pdbx_entity_src_syn.details ..._entity.pdbx_description / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _struct.pdbx_descriptor / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 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 Protein sprouty homolog 4
B: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)39,7762
Polymers39,7762
Non-polymers00
Water6,377354
1
A: 13-meric peptide from Protein sprouty homolog 4


Theoretical massNumber of molelcules
Total (without water)1,5841
Polymers1,5841
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


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-7.7 kcal/mol
Surface area14880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.851, 122.851, 55.537
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein/peptide 13-meric peptide from Protein sprouty homolog 4 / Spry-4 / Sprouty-4


Mass: 1583.527 Da / Num. of mol.: 1 / Fragment: UNP residues 46-58, pTyr-53 phosphopeptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9C004
#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.: 1
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.: 354 / 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: 3.04 Å3/Da / Density % sol: 59.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M NA/K TARTRATE, 20% PEG 3350, pH 7.5, 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: Mar 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 31352 / % possible obs: 96.3 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.052 / Χ2: 0.817 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.0713.70.15126550.41782.1
2.07-2.1514.20.13328530.45388.4
2.15-2.2515.10.11330390.50994.4
2.25-2.3716.10.131920.53898.5
2.37-2.5217.50.09132390.585100
2.52-2.7118.80.07732310.681100
2.71-2.9919.70.07332601.176100
2.99-3.4220.70.06132561.163100
3.42-4.31210.04432831.07199.9
4.31-5022.10.03733441.00399.5

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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: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2128 6.5 %RANDOM
Rwork0.201 ---
obs-31294 96.2 %-
Solvent computationBsol: 47.686 Å2
Displacement parametersBiso mean: 41.99 Å2
Baniso -1Baniso -2Baniso -3
1-13.038 Å23.791 Å20 Å2
2--13.038 Å20 Å2
3----26.076 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2552 0 0 354 2906
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.364
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ptr.param

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