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

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Basic information

Entry
Database: PDB / ID: 3buo
TitleCrystal structure of c-Cbl-TKB domain complexed with its binding motif in EGF receptor'
Components
  • 13-meric peptide from Epidermal growth factor receptor
  • E3 ubiquitin-protein ligase CBL
KeywordsLIGASE/SIGNALING PROTEIN / Cbl / TKB / ligase / signal transduction / proto-oncogene / complex / Anti-oncogene / ATP-binding / Cell cycle / Disease mutation / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Secreted / Transferase / Transmembrane / Tyrosine-protein kinase / Metal-binding / SH2 domain / Ubl conjugation pathway / 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 / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / regulation of peptidyl-tyrosine phosphorylation / epidermal growth factor binding / response to UV-A / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / PLCG1 events in ERBB2 signaling / Interleukin-6 signaling / ERBB2-EGFR signaling pathway / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / mast cell degranulation / response to starvation / ERBB2 Activates PTK6 Signaling / digestive tract morphogenesis / Signaling by EGFR / response to testosterone / intracellular vesicle / negative regulation of epidermal growth factor receptor signaling pathway / eyelid development in camera-type eye / cerebral cortex cell migration / protein insertion into membrane / ERBB2 Regulates Cell Motility / TGF-beta receptor signaling activates SMADs / protein tyrosine kinase activator activity / Respiratory syncytial virus (RSV) attachment and entry / Signaling by ERBB4 / PI3K events in ERBB2 signaling / positive regulation of phosphorylation / positive regulation of peptidyl-serine phosphorylation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / hair follicle development / protein monoubiquitination / MAP kinase kinase kinase activity / GAB1 signalosome / positive regulation of G1/S transition of mitotic cell cycle / FLT3 signaling by CBL mutants / embryonic placenta development / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / salivary gland morphogenesis / protein autoubiquitination / ephrin receptor binding / cellular response to platelet-derived growth factor stimulus / InlB-mediated entry of Listeria monocytogenes into host cell / Signaling by ERBB2 / phosphotyrosine residue binding / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / EGFR Transactivation by Gastrin / transmembrane receptor protein tyrosine kinase activity / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / ossification / NOTCH3 Activation and Transmission of Signal to the Nucleus / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / positive regulation of DNA repair / basal plasma membrane / cellular response to epidermal growth factor stimulus / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / EGFR downregulation / positive regulation of DNA replication / epithelial cell proliferation / response to activity / positive regulation of epithelial cell proliferation / Spry regulation of FGF signaling / Signal transduction by L1 / response to gamma radiation / Negative regulation of MET activity / positive regulation of protein localization to plasma membrane / cellular response to amino acid stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to estradiol stimulus / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Downregulation of ERBB2 signaling / cell-cell adhesion / Signaling by ERBB2 ECD mutants / receptor protein-tyrosine kinase / cellular response to nerve growth factor stimulus / Signaling by ERBB2 KD Mutants / receptor tyrosine kinase binding / negative regulation of protein catabolic process / RING-type E3 ubiquitin transferase
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 / 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) / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / SH2 domain / SHC Adaptor Protein / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / UBA-like superfamily / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Ring finger / Growth factor receptor cysteine-rich domain superfamily / : / Zinc finger RING-type profile. / 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
Epidermal growth factor receptor / E3 ubiquitin-protein ligase CBL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 1.2Jan 14, 2015Group: Derived calculations
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Sep 19, 2018Group: Data collection / Source and taxonomy
Category: diffrn_radiation / diffrn_radiation_wavelength / pdbx_entity_src_syn
Item: _diffrn_radiation.wavelength_id / _pdbx_entity_src_syn.details ..._diffrn_radiation.wavelength_id / _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
Revision 1.5Nov 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 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 13-meric peptide from Epidermal growth factor receptor
B: E3 ubiquitin-protein ligase CBL
C: 13-meric peptide from Epidermal growth factor receptor
D: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)79,4914
Polymers79,4914
Non-polymers00
Water4,234235
1
A: 13-meric peptide from Epidermal growth factor receptor
B: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)39,7462
Polymers39,7462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-7 kcal/mol
Surface area15050 Å2
MethodPISA
2
C: 13-meric peptide from Epidermal growth factor receptor
D: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)39,7462
Polymers39,7462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-7 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.862, 110.173, 55.821
Angle α, β, γ (deg.)90.000, 89.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide 13-meric peptide from Epidermal growth factor receptor / Receptor tyrosine-protein kinase ErbB-1 / EGFR


Mass: 1553.502 Da / Num. of mol.: 2 / Fragment: UNP residues 1063-1075, pTyr-1069 phosphopeptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P00533
#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.: 235 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.25M Na formate, 20% PEG 3350, pH 7.0, 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: 2.6→40 Å / Num. obs: 21945 / % possible obs: 91.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.109 / Χ2: 1.228 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.6920.33519840.728183
2.69-2.820.30520540.702185.7
2.8-2.932.10.27820620.717187.5
2.93-3.082.30.24121030.853188.7
3.08-3.282.50.221870.974192.1
3.28-3.532.70.16222381.155193.7
3.53-3.882.90.13322731.341196.2
3.88-4.443.20.09723091.461196.4
4.44-5.63.40.08323431.486197.5
5.6-403.70.05723921.574198.4

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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: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 4066
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1807 5.3 %RANDOM
Rwork0.231 ---
obs-17765 51.8 %-
Solvent computationBsol: 11.576 Å2
Displacement parametersBiso mean: 33.644 Å2
Baniso -1Baniso -2Baniso -3
1-7.709 Å20 Å20 Å2
2--15.362 Å20 Å2
3----23.071 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5170 0 0 235 5405
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.326
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ptr.param

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