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- PDB-3ob1: Crystal structure of c-Cbl TKB domain in complex with double phos... -

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Basic information

Entry
Database: PDB / ID: 3ob1
TitleCrystal structure of c-Cbl TKB domain in complex with double phosphorylated Spry2 peptide
Components
  • 12-meric peptide from Protein sprouty homolog 2
  • E3 ubiquitin-protein ligase CBL
KeywordsLigase/signaling Protein / protein-peptide complex / double phosphorylation / complex / E3 ubiquitin ligase / Spry2 / phosphorylation / Ligase-signaling Protein complex
Function / homology
Function and homology information


microtubule end / lung growth / negative regulation of lens fiber cell differentiation / negative regulation of cell projection organization / ubiquitin-protein transferase inhibitor activity / negative regulation of neurotrophin TRK receptor signaling pathway / bud elongation involved in lung branching / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / negative regulation of fibroblast growth factor receptor signaling pathway ...microtubule end / lung growth / negative regulation of lens fiber cell differentiation / negative regulation of cell projection organization / ubiquitin-protein transferase inhibitor activity / negative regulation of neurotrophin TRK receptor signaling pathway / bud elongation involved in lung branching / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of vascular endothelial growth factor signaling pathway / animal organ development / regulation of Rap protein signal transduction / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / negative regulation of Ras protein signal transduction / protein serine/threonine kinase inhibitor activity / inner ear morphogenesis / negative regulation of epithelial to mesenchymal transition / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling / response to starvation / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of peptidyl-threonine phosphorylation / cellular response to platelet-derived growth factor stimulus / TGF-beta receptor signaling activates SMADs / response to testosterone / establishment of mitotic spindle orientation / protein monoubiquitination / cell fate commitment / fibroblast growth factor receptor signaling pathway / cellular response to vascular endothelial growth factor stimulus / protein autoubiquitination / negative regulation of protein ubiquitination / FLT3 signaling by CBL mutants / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / phosphotyrosine residue binding / ephrin receptor binding / ERK1 and ERK2 cascade / negative regulation of angiogenesis / protein serine/threonine kinase activator activity / cellular response to nerve growth factor stimulus / InlB-mediated entry of Listeria monocytogenes into host cell / response to gamma radiation / cellular response to leukemia inhibitory factor / response to activity / Regulation of signaling by CBL / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / EGFR downregulation / Negative regulation of FGFR4 signaling / sensory perception of sound / negative regulation of transforming growth factor beta receptor signaling pathway / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / Constitutive Signaling by EGFRvIII / RING-type E3 ubiquitin transferase / Negative regulation of MET activity / cilium / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / cytokine-mediated signaling pathway / SH3 domain binding / ruffle membrane / positive regulation of receptor-mediated endocytosis / protein polyubiquitination / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin-protein transferase activity / male gonad development / microtubule cytoskeleton / ubiquitin protein ligase activity / actin cytoskeleton / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / cellular response to hypoxia / growth cone / ubiquitin-dependent protein catabolic process / response to ethanol / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / protein ubiquitination / positive regulation of cell migration / cadherin binding / symbiont entry into host cell / membrane raft / negative regulation of cell population proliferation / focal adhesion / DNA damage response / calcium ion binding / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus
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 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / 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
Protein sprouty homolog 2 / E3 ubiquitin-protein ligase CBL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSun, Q. / Sivaraman, J.
CitationJournal: Plos One / Year: 2010
Title: Additional serine/threonine phosphorylation reduces binding affinity but preserves interface topography of substrate proteins to the c-Cbl TKB domain
Authors: Sun, Q. / Jackson, R.A. / Ng, C. / Guy, G.R. / Sivaraman, J.
History
DepositionAug 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 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 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 12-meric peptide from Protein sprouty homolog 2
B: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)39,7482
Polymers39,7482
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-8 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.092, 122.092, 55.689
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-32-

HOH

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Components

#1: Protein/peptide 12-meric peptide from Protein sprouty homolog 2 / Spry-2


Mass: 1555.411 Da / Num. of mol.: 1 / Fragment: residues 49-60 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: O43597
#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, residues 25-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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.: 162 / 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: 3.01 Å3/Da / Density % sol: 59.2 % / Mosaicity: 0.68 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2M K/Na tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER PROTEUM X8 / Wavelength: 1.5418 Å
DetectorType: BRUKER AXS MICROSTAR / Detector: CCD / Date: Jun 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 31335 / % possible obs: 99.5 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.091 / Χ2: 1.01 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.02-2.094.80.4630491.02998.1
2.09-2.185.60.39731111.01199.2
2.18-2.2760.3513093199.3
2.27-2.396.70.29731081.01399.3
2.39-2.547.40.23831281.02999.7
2.54-2.748.40.18831191.04999.6
2.74-3.029.50.14631351.0499.8
3.02-3.45120.09531751.02299.9
3.45-4.3514.90.06831711.01999.9
4.35-5016.60.05132460.949100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BUM

3bum


Resolution: 2.2→49.27 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0 / SU B: 9.186 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22296 1235 5.1 %RANDOM
Rwork0.18095 ---
obs0.18303 24185 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.91 Å2 / Biso mean: 26.064 Å2 / Biso min: 3.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å20 Å2
2---0.32 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 0 162 2686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222592
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.9663505
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39223.387124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.65215461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8361518
X-RAY DIFFRACTIONr_chiral_restr0.1150.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211963
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0221.51529
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.02222475
X-RAY DIFFRACTIONr_scbond_it3.31831063
X-RAY DIFFRACTIONr_scangle_it5.3324.51030
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 85 -
Rwork0.209 1666 -
all-1751 -
obs--99.21 %
Refinement TLS params.Method: refined / Origin x: -56.595 Å / Origin y: 14.627 Å / Origin z: 0.278 Å
111213212223313233
T0.0311 Å20.0016 Å20.0194 Å2-0.0121 Å2-0.0074 Å2--0.028 Å2
L0.2353 °20.0017 °2-0.0085 °2-0.367 °2-0.1391 °2--0.1671 °2
S-0.0155 Å °0.025 Å °-0.0289 Å °-0.0291 Å °-0.025 Å °-0.0421 Å °0.0345 Å °-0.0129 Å °0.0406 Å °

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