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- PDB-3vrp: Crystal structure of the tyrosine kinase binding domain of Cbl-c ... -

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Basic information

Entry
Database: PDB / ID: 3vrp
TitleCrystal structure of the tyrosine kinase binding domain of Cbl-c in complex with phospho-EGFR peptide
Components
  • Epidermal growth factor receptor
  • Signal transduction protein CBL-C
KeywordsPROTEIN BINDING/Transferase / PTB domain / TKB (tyrosine kinase binding) domain / four-helix bundle (4H) / calcium-binding EF hand / divergent SH2 domain / Regulator of EGFR mediated signal transduction / Ubiquitously expressed / PROTEIN BINDING-Transferase complex
Function / homology
Function and homology information


response to glial cell derived neurotrophic factor / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / epidermal growth factor receptor binding / 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 ...response to glial cell derived neurotrophic factor / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / epidermal growth factor receptor binding / 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 / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / digestive tract morphogenesis / Signaling by EGFR / 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 / 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 / MAP kinase kinase kinase activity / GAB1 signalosome / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / salivary gland morphogenesis / negative regulation of MAPK cascade / Signaling by ERBB2 / phosphotyrosine residue binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / transmembrane receptor protein tyrosine kinase activity / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / ossification / SHC1 events in ERBB2 signaling / basal plasma membrane / positive regulation of DNA repair / cellular response to epidermal growth factor stimulus / positive regulation of DNA replication / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Signal transduction by L1 / positive regulation of protein localization to plasma membrane / NOTCH3 Activation and Transmission of Signal to the Nucleus / cellular response to amino acid stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to estradiol stimulus / EGFR downregulation / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / cell-cell adhesion / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / receptor tyrosine kinase binding / RING-type E3 ubiquitin transferase / negative regulation of protein catabolic process / Signaling by ERBB2 KD Mutants / SH3 domain binding / positive regulation of miRNA transcription / kinase binding / ruffle membrane / Downregulation of ERBB2 signaling / epidermal growth factor receptor signaling pathway / positive regulation of protein phosphorylation / cell morphogenesis / positive regulation of fibroblast proliferation / neuron differentiation / HCMV Early Events / Constitutive Signaling by Aberrant PI3K in Cancer / actin filament binding / ubiquitin protein ligase activity / cell junction / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / virus receptor activity / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / double-stranded DNA binding / protein tyrosine kinase activity
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 / Zinc finger, C3HC4 type (RING finger) / SH2 domain / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / SHC Adaptor Protein / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / 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-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.52 Å
AuthorsTakeshita, K. / Tezuka, T. / Isozaki, Y. / Yamashita, E. / Suzuki, M. / Yamanashi, Y. / Yamamoto, T. / Nakagawa, A.
CitationJournal: J.Biochem. / Year: 2012
Title: Structural flexibility regulates phosphopeptide-binding activity of the tyrosine kinase binding domain of Cbl-c.
Authors: Takeshita, K. / Tezuka, T. / Isozaki, Y. / Yamashita, E. / Suzuki, M. / Kim, M. / Yamanashi, Y. / Yamamoto, T. / Nakagawa, A.
History
DepositionApr 13, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Signal transduction protein CBL-C
B: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3573
Polymers38,3172
Non-polymers401
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-21 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.357, 108.710, 54.936
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-722-

HOH

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Components

#1: Protein Signal transduction protein CBL-C / RING finger protein 57 / SH3-binding protein CBL-3 / SH3-binding protein CBL-C


Mass: 36691.070 Da / Num. of mol.: 1 / Fragment: tyrosine kinase binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBLC / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: Q9ULV8
#2: Protein/peptide Epidermal growth factor receptor / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1


Mass: 1625.564 Da / Num. of mol.: 1
Fragment: phospho-EGFR peptide, UNP residues residues 1062-1074
Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human)
References: UniProt: P00533, receptor protein-tyrosine kinase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 1.82 Å3/Da / Density % sol: 32.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG3350, 0.1M ammonium formate, 0.2M NDSB-201, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Dec 2, 2007
Diffraction measurementDetails: 1.00 degrees, 10.0 sec, detector distance 250.00 mm
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionAv R equivalents: 0.06 / Number: 248267
ReflectionResolution: 1.52→50 Å / Num. obs: 43495 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 33.698
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 4.16 / Rsym value: 0.492 / % possible all: 100
Cell measurementReflection used: 248267

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.68 Å33.78 Å
Translation1.68 Å33.78 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→33.78 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.229 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.08 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2187 5 %RANDOM
Rwork0.1773 ---
obs0.1789 43450 99.83 %-
all-3137 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.07 Å2 / Biso mean: 17.8864 Å2 / Biso min: 4.18 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.52→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 1 291 2640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222418
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.9693286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1635297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07222.336107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02915385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1391522
X-RAY DIFFRACTIONr_chiral_restr0.1090.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211858
X-RAY DIFFRACTIONr_mcbond_it1.2451.51494
X-RAY DIFFRACTIONr_mcangle_it2.22822395
X-RAY DIFFRACTIONr_scbond_it3.2933924
X-RAY DIFFRACTIONr_scangle_it5.1274.5891
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.518-1.5580.2381670.20429703190313798.339
1.558-1.60.2231630.191291130743074100
1.6-1.6460.241530.18428563010300999.967
1.646-1.6970.2651530.19227692924292299.932
1.697-1.7530.2271470.18327012849284899.965
1.753-1.8140.1961400.17125932735273399.927
1.814-1.8820.2091310.17325392671267099.963
1.882-1.9590.1871250.172244725722572100
1.959-2.0460.1981300.17223402471247099.96
2.046-2.1450.2131060.173222423302330100
2.145-2.260.1711010.166214522462246100
2.26-2.3970.2191120.16620192132224499.953
2.397-2.5620.205870.168191520022002100
2.562-2.7650.2411050.192176918741874100
2.765-3.0270.223860.17916431730172999.942
3.027-3.3810.196710.17115031575157499.937
3.381-3.8980.18760.16613291406140599.929
3.898-4.7580.217580.15911401199119899.917
4.758-6.6630.198570.20688894694599.894
6.663-33.7810.222190.21856258658199.147

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