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

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Basic information

Entry
Database: PDB / ID: 3bux
TitleCrystal structure of c-Cbl-TKB domain complexed with its binding motif in c-Met
Components
  • 13-meric peptide from Hepatocyte growth factor receptor
  • E3 ubiquitin-protein ligase CBL
KeywordsLIGASE/SIGNALING PROTEIN / Cbl / TKB / ligase / signal transduction / proto-oncogene / complex / ATP-binding / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transferase / Transmembrane / Tyrosine-protein kinase / Calcium / Cytoplasm / Metal-binding / SH2 domain / Ubl conjugation pathway / Zinc / 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 / hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / endothelial cell morphogenesis / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / semaphorin receptor activity / MET receptor recycling / pancreas development / MET activates PTPN11 / MET activates RAP1 and RAC1 / Sema4D mediated inhibition of cell attachment and migration / MET activates PI3K/AKT signaling / negative regulation of stress fiber assembly / positive regulation of endothelial cell chemotaxis / negative regulation of Rho protein signal transduction / positive regulation of epidermal growth factor receptor signaling pathway / MET activates PTK2 signaling / Regulation of KIT signaling / branching morphogenesis of an epithelial tube / mast cell degranulation / Interleukin-6 signaling / positive chemotaxis / response to starvation / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of thrombin-activated receptor signaling pathway / cellular response to platelet-derived growth factor stimulus / response to testosterone / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / semaphorin-plexin signaling pathway / establishment of skin barrier / protein autoubiquitination / MET activates RAS signaling / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / phagocytosis / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / FLT3 signaling by CBL mutants / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / ephrin receptor binding / phosphotyrosine residue binding / negative regulation of autophagy / basal plasma membrane / cellular response to nerve growth factor stimulus / InlB-mediated entry of Listeria monocytogenes into host cell / excitatory postsynaptic potential / liver development / molecular function activator activity / response to activity / response to gamma radiation / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / EGFR downregulation / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Constitutive Signaling by EGFRvIII / Spry regulation of FGF signaling / RING-type E3 ubiquitin transferase / Negative regulation of MET activity / receptor protein-tyrosine kinase / neuron differentiation / cilium / receptor tyrosine kinase binding / cytokine-mediated signaling pathway / positive regulation of receptor-mediated endocytosis / SH3 domain binding / protein polyubiquitination / ubiquitin-protein transferase activity / Signaling by CSF1 (M-CSF) in myeloid cells / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / ubiquitin protein ligase activity / cell migration / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / nervous system development / cellular response to hypoxia / growth cone / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / ubiquitin-dependent protein catabolic process / protein tyrosine kinase activity / protein phosphatase binding / response to ethanol / postsynapse / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell surface 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 / Tyrosine-protein kinase, HGF/MSP receptor / Transcription Elongation Factor S-II; Chain A / Plexin family / UBA/TS-N domain / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin associated domain / ig-like, plexins, transcription factors / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / PSI domain / domain found in Plexins, Semaphorins and Integrins / SH2 domain / SHC Adaptor Protein / IPT domain / 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 / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Immunoglobulin E-set / 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 / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / 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
Hepatocyte growth factor receptor / E3 ubiquitin-protein ligase CBL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 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 1.2Oct 25, 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 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 Hepatocyte growth factor receptor
B: E3 ubiquitin-protein ligase CBL
C: 13-meric peptide from Hepatocyte growth factor receptor
D: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)79,5754
Polymers79,5754
Non-polymers00
Water12,358686
1
A: 13-meric peptide from Hepatocyte growth factor receptor


Theoretical massNumber of molelcules
Total (without water)1,5961
Polymers1,5961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)38,1921
Polymers38,1921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 13-meric peptide from Hepatocyte growth factor receptor


Theoretical massNumber of molelcules
Total (without water)1,5961
Polymers1,5961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)38,1921
Polymers38,1921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: 13-meric peptide from Hepatocyte growth factor receptor
B: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)39,7882
Polymers39,7882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-5.4 kcal/mol
Surface area14820 Å2
MethodPISA
6
C: 13-meric peptide from Hepatocyte growth factor receptor
D: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)39,7882
Polymers39,7882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-5.5 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.175, 104.800, 52.598
Angle α, β, γ (deg.)90.000, 90.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide 13-meric peptide from Hepatocyte growth factor receptor / HGF receptor / Scatter factor receptor / SF receptor / HGF/SF receptor / Met proto-oncogene ...HGF receptor / Scatter factor receptor / SF receptor / HGF/SF receptor / Met proto-oncogene tyrosine kinase / c-Met


Mass: 1595.537 Da / Num. of mol.: 2 / Fragment: UNP residues 997-1009, pTyr-1003 phosphopeptide / Source method: obtained synthetically / Details: synthetic construct / References: UniProt: P08581
#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.: 686 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.15M malic acid, 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: 1.35→50 Å / Num. obs: 142289 / % possible obs: 95 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.04 / Χ2: 0.608 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.35-1.44.90.236130010.35587.2
1.4-1.455.50.203137140.36391.8
1.45-1.5260.156140430.39893.9
1.52-1.66.30.119141380.43994.5
1.6-1.76.60.087142860.44795.4
1.7-1.836.80.067144040.48796.3
1.83-2.0270.053144780.61296.7
2.02-2.317.20.044146030.82297.6
2.31-2.917.20.034147910.7998.3
2.91-507.60.03148311.03697.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.6 Å29.1 Å
Translation1.6 Å29.1 Å

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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: 1.35→20 Å / Cross valid method: THROUGHOUT / σ(F): 11808
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2208 1.5 %RANDOM
Rwork0.225 ---
obs-130160 87 %-
Solvent computationBsol: 52.376 Å2
Displacement parametersBiso mean: 18.448 Å2
Baniso -1Baniso -2Baniso -3
1--3.011 Å20 Å20.733 Å2
2--1.438 Å20 Å2
3---1.573 Å2
Refinement stepCycle: LAST / Resolution: 1.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5134 0 0 686 5820
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.112
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ptr.param

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