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

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Basic information

Entry
Database: PDB / ID: 3vro
TitleCrystal structure of the tyrosine kinase binding domain of Cbl-c in complex with phospho-Src peptide
Components
  • Proto-oncogene tyrosine-protein kinase Src
  • 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 / regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / regulation of cell projection assembly / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to prolactin / positive regulation of male germ cell proliferation / dendritic filopodium / negative regulation of telomere maintenance / response to mineralocorticoid ...response to glial cell derived neurotrophic factor / regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / regulation of cell projection assembly / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to prolactin / positive regulation of male germ cell proliferation / dendritic filopodium / negative regulation of telomere maintenance / response to mineralocorticoid / Regulation of commissural axon pathfinding by SLIT and ROBO / positive regulation of dephosphorylation / regulation of epithelial cell migration / ERBB2 signaling pathway / positive regulation of protein transport / Regulation of gap junction activity / cellular response to progesterone stimulus / BMP receptor binding / negative regulation of focal adhesion assembly / positive regulation of protein processing / skeletal muscle cell proliferation / positive regulation of integrin activation / Activated NTRK2 signals through FYN / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / regulation of vascular permeability / negative regulation of neutrophil activation / positive regulation of glucose metabolic process / transcytosis / osteoclast development / Activated NTRK3 signals through PI3K / connexin binding / focal adhesion assembly / cellular response to fluid shear stress / adherens junction organization / signal complex assembly / positive regulation of small GTPase mediated signal transduction / Co-stimulation by CD28 / branching involved in mammary gland duct morphogenesis / response to acidic pH / positive regulation of Ras protein signal transduction / Regulation of RUNX1 Expression and Activity / DCC mediated attractive signaling / positive regulation of podosome assembly / EPH-Ephrin signaling / regulation of bone resorption / positive regulation of lamellipodium morphogenesis / Ephrin signaling / myoblast proliferation / Signal regulatory protein family interactions / cellular response to peptide hormone stimulus / negative regulation of mitochondrial depolarization / epidermal growth factor receptor binding / podosome / odontogenesis / MET activates PTK2 signaling / cellular response to fatty acid / Regulation of KIT signaling / postsynaptic specialization, intracellular component / regulation of early endosome to late endosome transport / Signaling by ALK / leukocyte migration / phospholipase activator activity / Co-inhibition by CTLA4 / oogenesis / GP1b-IX-V activation signalling / Receptor Mediated Mitophagy / EPHA-mediated growth cone collapse / interleukin-6-mediated signaling pathway / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / DNA biosynthetic process / positive regulation of Notch signaling pathway / Signaling by EGFR / stress fiber assembly / RUNX2 regulates osteoblast differentiation / stimulatory C-type lectin receptor signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / uterus development / regulation of cell-cell adhesion / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase binding / PECAM1 interactions / Recycling pathway of L1 / regulation of heart rate by cardiac conduction / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / dendritic growth cone / protein tyrosine kinase activator activity / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / negative regulation of anoikis / RET signaling / Long-term potentiation / FCGR activation / positive regulation of epithelial cell migration / EPH-ephrin mediated repulsion of cells / ephrin receptor 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 / Transcription Elongation Factor S-II; Chain A / Zinc finger, C3HC4 type (RING finger) / SH2 domain / SHC Adaptor Protein / : / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Ring finger / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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
Proto-oncogene tyrosine-protein kinase Src / E3 ubiquitin-protein ligase CBL-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 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: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3783
Polymers38,3382
Non-polymers401
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-20 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.282, 108.493, 54.761
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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 Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 1646.652 Da / Num. of mol.: 1 / Fragment: phospho-Src peptide, residues 412-424 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human)
References: UniProt: P12931, non-specific 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.: 204 / 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: 1.81 Å3/Da / Density % sol: 31.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG3350, 0.1M ammonium formate, 0.1M 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 301.198 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: 0.082 / Number: 135096
ReflectionResolution: 1.8→50 Å / Num. obs: 26228 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 21.609
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.8-1.835.20.5383.28312810.538100
1.83-1.865.20.4683.77512780.468100
1.86-1.95.20.4313.99812980.431100
1.9-1.945.20.3644.64812930.364100
1.94-1.985.20.3055.81312930.305100
1.98-2.035.20.2477.16712970.247100
2.03-2.085.20.2237.98113050.22399.9
2.08-2.135.20.1929.11312850.192100
2.13-2.25.20.15511.2213140.155100
2.2-2.275.20.14212.17112830.142100
2.27-2.355.20.12214.71913060.122100
2.35-2.445.20.10117.413080.101100
2.44-2.555.20.08420.64113040.084100
2.55-2.695.20.07722.50413070.077100
2.69-2.865.20.06925.48613250.069100
2.86-3.085.20.05631.21213110.056100
3.08-3.395.20.04638.45913300.046100
3.39-3.885.10.03847.34713350.038100
3.88-4.8850.03253.86213460.032100
4.88-504.70.03353.42514290.03399.8
Cell measurementReflection used: 135096

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.98 Å35.37 Å
Translation1.98 Å35.37 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.89 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.1937 / WRfactor Rwork: 0.1561 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8741 / SU B: 2.448 / SU ML: 0.077 / SU R Cruickshank DPI: 0.124 / SU Rfree: 0.1228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 1332 5.1 %RANDOM
Rwork0.1656 ---
obs0.168 26211 99.72 %-
all-1830 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 64.68 Å2 / Biso mean: 18.1847 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 1 204 2479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222347
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.9693186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2935288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2322.404104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37215381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0811521
X-RAY DIFFRACTIONr_chiral_restr0.1340.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211791
X-RAY DIFFRACTIONr_mcbond_it1.3521.51448
X-RAY DIFFRACTIONr_mcangle_it2.522320
X-RAY DIFFRACTIONr_scbond_it3.8963899
X-RAY DIFFRACTIONr_scangle_it6.2174.5866
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 (%)
1.797-1.8430.277840.21817461830183096.21
1.843-1.8930.194870.1891855100
1.893-1.9480.1861010.1811809100
1.948-2.0080.166910.1641751100
2.008-2.0730.16660.158171599.942
2.073-2.1460.164720.1611674100
2.146-2.2260.157970.1541586100
2.226-2.3170.145820.1411560100
2.317-2.4190.179790.1761474100
2.419-2.5360.166850.1621411100
2.536-2.6720.172680.1691357100
2.672-2.8330.179670.1771290100
2.833-3.0270.168660.1641217100
3.027-3.2660.157650.1551140100
3.266-3.5740.161490.1611048100
3.574-3.9890.144460.144952100
3.989-4.5920.146380.144846100
4.592-5.5910.169380.17745100
5.591-7.7720.212370.208583100
7.772-29.8910.193140.19369100

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