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

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Basic information

Entry
Database: PDB / ID: 3vrn
TitleCrystal structure of the tyrosine kinase binding domain of Cbl-c
ComponentsSignal transduction protein CBL-C
KeywordsPROTEIN BINDING / 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
Function / homology
Function and homology information


negative regulation of epidermal growth factor-activated receptor activity / epidermal growth factor receptor binding / negative regulation of epidermal growth factor receptor signaling pathway / phosphotyrosine residue binding / negative regulation of MAP kinase activity / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / SH3 domain binding / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process ...negative regulation of epidermal growth factor-activated receptor activity / epidermal growth factor receptor binding / negative regulation of epidermal growth factor receptor signaling pathway / phosphotyrosine residue binding / negative regulation of MAP kinase activity / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / SH3 domain binding / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / cell surface receptor signaling pathway / protein ubiquitination / membrane raft / calcium ion binding / signal transduction / zinc ion binding / plasma membrane
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 / 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-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 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 8, 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 / 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_asym_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_asym_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

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Assembly

Deposited unit
A: Signal transduction protein CBL-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7312
Polymers36,6911
Non-polymers401
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.223, 107.617, 54.773
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: TKB 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: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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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: 1.87 Å3/Da / Density % sol: 34.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% 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: Jun 25, 2007
Diffraction measurementDetails: 1.00 degrees, 10.0 sec, detector distance 300.00 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: 0.054 / Number: 148076
ReflectionResolution: 1.64→50 Å / Num. obs: 34203 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 27.992
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.64-1.674.30.4463.45216880.446100
1.67-1.74.30.43.84317100.4100
1.7-1.734.30.3554.4116510.355100
1.73-1.774.30.2995.2217180.299100
1.77-1.814.30.2815.6116640.28199.9
1.81-1.854.30.2316.9416810.231100
1.85-1.894.40.1997.84317050.187100
1.89-1.944.30.1669.56516960.153100
1.94-24.40.13311.81616930.1299.9
2-2.074.40.11114.09916750.104100
2.07-2.144.40.09516.64217180.08999.9
2.14-2.234.40.07820.18216900.075100
2.23-2.334.40.06922.1817090.06799.9
2.33-2.454.40.05926.03817220.058100
2.45-2.64.40.05229.6216980.05199.9
2.6-2.84.40.04731.86717190.047100
2.8-3.094.40.03838.08317370.039100
3.09-3.534.30.03244.9117230.035100
3.53-4.454.30.02850.78417630.032100
4.45-504.10.02750.87918430.03299.8
Cell measurementReflection used: 148076

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.82 Å43.24 Å
Translation1.82 Å43.24 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
Starting model: 2CBL

2cbl


Resolution: 1.64→43.24 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.177 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.744 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2177 1728 5.1 %RANDOM
Rwork0.1816 ---
obs0.1834 34184 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.24 Å2 / Biso mean: 20.2597 Å2 / Biso min: 6.26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.64→43.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 1 239 2510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222331
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.9663165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3165287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36222.255102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69715373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0631521
X-RAY DIFFRACTIONr_chiral_restr0.1270.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211789
X-RAY DIFFRACTIONr_mcbond_it1.3581.51443
X-RAY DIFFRACTIONr_mcangle_it2.40422310
X-RAY DIFFRACTIONr_scbond_it3.7273888
X-RAY DIFFRACTIONr_scangle_it5.7274.5855
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 (%)
1.638-1.6810.3211140.22723182489220497.71
1.681-1.7270.2481400.20323142455217499.959
1.727-1.7770.2491140.204224023542126100
1.777-1.8320.2471140.19222032318208999.957
1.832-1.8920.2751100.181210722171997100
1.892-1.9580.219970.17206821651971100
1.958-2.0320.2221120.16519822095187099.952
2.032-2.1140.208950.178192220171827100
2.114-2.2080.2191170.17818061924168999.948
2.208-2.3160.225910.17517681860167799.946
2.316-2.440.225890.174166417531575100
2.44-2.5880.199880.17615981687151099.941
2.588-2.7660.227770.18914921570141599.936
2.766-2.9860.226760.195141014861334100
2.986-3.270.166740.175128713611213100
3.27-3.6530.204740.169116812421094100
3.653-4.2130.18530.158105711101004100
4.213-5.1480.208330.17290493887199.893
5.148-7.230.29350.225717752682100
7.23-43.2440.191250.20643145740699.781

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