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

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Basic information

Entry
Database: PDB / ID: 3bum
TitleCrystal structure of c-Cbl-TKB domain complexed with its binding motif in Sprouty2
Components
  • E3 ubiquitin-protein ligase CBL
  • Protein sprouty homolog 2
KeywordsLIGASE / signal transduction / proto-oncogene / complex / Cytoplasm / Developmental protein / Membrane / Microtubule / Polymorphism / Calcium / Metal-binding / Phosphoprotein / SH2 domain / Ubl conjugation pathway / Zinc / Zinc-finger
Function / homology
Function and homology information


microtubule end / negative regulation of cell projection organization / negative regulation of lens fiber cell differentiation / lung growth / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of vascular endothelial growth factor signaling pathway / animal organ development / negative regulation of fibroblast growth factor receptor signaling pathway / ubiquitin-dependent endocytosis ...microtubule end / negative regulation of cell projection organization / negative regulation of lens fiber cell differentiation / lung growth / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of vascular endothelial growth factor signaling pathway / animal organ development / negative regulation of fibroblast growth factor receptor signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / ubiquitin-protein transferase inhibitor activity / bud elongation involved in lung branching / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / negative regulation of Ras protein signal transduction / Regulation of KIT signaling / negative regulation of epithelial to mesenchymal transition / positive regulation of epidermal growth factor receptor signaling pathway / inner ear morphogenesis / mast cell degranulation / Interleukin-6 signaling / response to starvation / response to testosterone / negative regulation of epidermal growth factor receptor signaling pathway / TGF-beta receptor signaling activates SMADs / establishment of mitotic spindle orientation / protein serine/threonine kinase inhibitor activity / positive regulation of peptidyl-serine phosphorylation / cellular response to vascular endothelial growth factor stimulus / cell fate commitment / fibroblast growth factor receptor signaling pathway / protein monoubiquitination / FLT3 signaling by CBL mutants / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / protein autoubiquitination / cellular response to platelet-derived growth factor stimulus / InlB-mediated entry of Listeria monocytogenes into host cell / ephrin receptor binding / ERK1 and ERK2 cascade / phosphotyrosine residue binding / negative regulation of protein ubiquitination / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / negative regulation of angiogenesis / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / EGFR downregulation / protein serine/threonine kinase activator activity / cellular response to leukemia inhibitory factor / response to activity / Spry regulation of FGF signaling / response to gamma radiation / Negative regulation of MET activity / negative regulation of transforming growth factor beta receptor signaling pathway / sensory perception of sound / cellular response to nerve growth factor stimulus / Constitutive Signaling by EGFRvIII / negative regulation of ERK1 and ERK2 cascade / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / positive regulation of receptor-mediated endocytosis / Signaling by CSF1 (M-CSF) in myeloid cells / SH3 domain binding / ruffle membrane / cytokine-mediated signaling pathway / male gonad development / protein polyubiquitination / ubiquitin-protein transferase activity / Cargo recognition for clathrin-mediated endocytosis / ubiquitin protein ligase activity / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / actin cytoskeleton / microtubule cytoskeleton / growth cone / ubiquitin-dependent protein catabolic process / response to ethanol / cellular response to hypoxia / cytoskeleton / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cilium / positive regulation of cell migration / cadherin binding / membrane raft / negative regulation of cell population proliferation / focal adhesion / calcium ion binding / DNA damage response / positive regulation of gene expression / symbiont entry into host cell / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction
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 / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsNg, C. / Jackson, A.R. / Buschdorf, P.J. / Sun, Q. / Guy, R.G. / 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 16, 2020Group: Database references / Derived calculations / Structure summary
Category: entity / struct ...entity / struct / struct_conn / struct_ref_seq_dif
Item: _entity.pdbx_description / _struct.pdbx_descriptor ..._entity.pdbx_description / _struct.pdbx_descriptor / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 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: Protein sprouty homolog 2
B: E3 ubiquitin-protein ligase CBL


Theoretical massNumber of molelcules
Total (without water)39,7672
Polymers39,7672
Non-polymers00
Water5,350297
1
A: Protein sprouty homolog 2


Theoretical massNumber of molelcules
Total (without water)1,5751
Polymers1,5751
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


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-10 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.256, 122.256, 54.707
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein/peptide Protein sprouty homolog 2 / Spry-2


Mass: 1574.562 Da / Num. of mol.: 1 / Fragment: UNP residues 49-61
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPRY2 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / 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, UNP residues 25-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 / 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.: 297 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, PEG3350, pH7.5, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorDetector: CCD / Date: Sep 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 32750 / % possible obs: 99.9 % / Redundancy: 16.2 % / Rmerge(I) obs: 0.083 / Χ2: 1.162 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.98-2.058.20.34632350.54699.1
2.05-2.1312.10.32832450.615100
2.13-2.2313.60.27232490.704100
2.23-2.3514.50.2332550.764100
2.35-2.4915.70.1932800.8499.9
2.49-2.69170.14832320.92399.9
2.69-2.96180.11332801.038100
2.96-3.3919.80.07632841.253100
3.39-4.2621.20.06433061.95100
4.26-5021.10.05233841.854100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CBL

2cbl


Resolution: 2→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.263 2221 7 %
Rwork0.224 --
obs-31690 99.9 %
Solvent computationBsol: 55.439 Å2
Displacement parametersBiso mean: 31.025 Å2
Baniso -1Baniso -2Baniso -3
1-1.778 Å2-0.579 Å20 Å2
2--1.778 Å20 Å2
3----3.556 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 0 297 2860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.236
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ptr.param

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