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- PDB-5axi: Crystal structure of Cbl-b TKB domain in complex with Cblin -

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Basic information

Entry
Database: PDB / ID: 5axi
TitleCrystal structure of Cbl-b TKB domain in complex with Cblin
Components
  • Cblin
  • E3 ubiquitin-protein ligase CBL-B
KeywordsLIGASE/LIGASE inhibitor / Ubquitin ligase / phosphopeptide / cblin / LIGASE-LIGASE inhibitor complex
Function / homology
Function and homology information


peptidyl-amino acid modification / IRS-mediated signalling / Signaling by ALK / IRS-related events triggered by IGF1R / SOS-mediated signalling / negative regulation of alpha-beta T cell proliferation / PI3K/AKT activation / PI3K Cascade / negative regulation of somatostatin secretion / positive regulation of glucagon secretion ...peptidyl-amino acid modification / IRS-mediated signalling / Signaling by ALK / IRS-related events triggered by IGF1R / SOS-mediated signalling / negative regulation of alpha-beta T cell proliferation / PI3K/AKT activation / PI3K Cascade / negative regulation of somatostatin secretion / positive regulation of glucagon secretion / IRS activation / Interleukin-7 signaling / regulation of T cell receptor signaling pathway / negative regulation of epidermal growth factor-activated receptor activity / Signal attenuation / epithelial cell migration / regulation of platelet-derived growth factor receptor-alpha signaling pathway / RAF/MAP kinase cascade / positive regulation of T cell anergy / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of fatty acid beta-oxidation / phosphatidylinositol 3-kinase activator activity / regulation of protein binding / Antigen processing: Ubiquitination & Proteasome degradation / mammary gland development / insulin receptor complex / positive regulation of glucose metabolic process / transmembrane receptor protein tyrosine kinase adaptor activity / response to caffeine / positive regulation of mesenchymal cell proliferation / cellular response to fatty acid / negative regulation of T cell receptor signaling pathway / regulation of GTPase activity / positive regulation of epithelial cell migration / protein localization to nucleus / negative regulation of insulin secretion / positive regulation of glycogen biosynthetic process / phosphatidylinositol 3-kinase binding / lipid catabolic process / regulation of cell adhesion / positive regulation of insulin receptor signaling pathway / positive regulation of phosphorylation / negative regulation of insulin receptor signaling pathway / insulin-like growth factor receptor binding / phosphotyrosine residue binding / SH2 domain binding / T cell activation / insulin-like growth factor receptor signaling pathway / ciliary basal body / protein kinase C binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein ubiquitination / caveola / positive regulation of glucose import / response to insulin / RING-type E3 ubiquitin transferase / insulin receptor binding / receptor tyrosine kinase binding / SH3 domain binding / cytokine-mediated signaling pathway / cellular response to insulin stimulus / positive regulation of protein catabolic process / ubiquitin protein ligase activity / cell migration / signaling receptor complex adaptor activity / protein-macromolecule adaptor activity / insulin receptor signaling pathway / T cell receptor signaling pathway / regulation of gene expression / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / immune response / membrane raft / protein domain specific binding / calcium ion binding / protein-containing complex binding / protein kinase binding / signal transduction / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Insulin receptor substrate / E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Adaptor protein Cbl, N-terminal domain / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain ...Insulin receptor substrate / E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / 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. / Phosphotyrosine-binding domain / Adaptor protein Cbl, N-terminal domain superfamily / Transcription Elongation Factor S-II; Chain A / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / SH2 domain / SHC Adaptor Protein / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PH domain / Recoverin; domain 1 / Ring finger / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Insulin receptor substrate 1 / E3 ubiquitin-protein ligase CBL-B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOhno, A. / Maita, N. / Ochi, A. / Nakao, R. / Nikawa, T.
CitationJournal: Arch.Biochem.Biophys. / Year: 2016
Title: Structural analysis of the TKB domain of ubiquitin ligase Cbl-b complexed with its small inhibitory peptide, Cblin
Authors: Ohno, A. / Ochi, A. / Maita, N. / Ueji, T. / Bando, A. / Nakao, R. / Hirasaka, K. / Abe, T. / Teshima-Kondo, S. / Nemoto, H. / Okumura, Y. / Higashibata, A. / Yano, S. / Tochio, H. / Nikawa, T.
History
DepositionJul 29, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase CBL-B
B: E3 ubiquitin-protein ligase CBL-B
C: E3 ubiquitin-protein ligase CBL-B
E: Cblin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,64811
Polymers108,3864
Non-polymers2627
Water3,009167
1
A: E3 ubiquitin-protein ligase CBL-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0555
Polymers35,9081
Non-polymers1464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-23 kcal/mol
Surface area15370 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase CBL-B
E: Cblin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6454
Polymers36,5702
Non-polymers762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-19 kcal/mol
Surface area15570 Å2
MethodPISA
3
C: E3 ubiquitin-protein ligase CBL-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9482
Polymers35,9081
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.144, 94.091, 133.949
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase CBL-B / Casitas B-lineage lymphoma proto-oncogene b / SH3-binding protein CBL-B / Signal transduction protein CBL-B


Mass: 35908.199 Da / Num. of mol.: 3 / Fragment: UNP residues 38-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cblb / Plasmid: pGEM4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q3TTA7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Cblin


Mass: 661.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: IRS-1 / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P35569*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, BIS-TRIS, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 35370 / Num. obs: 35334 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 15.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.069 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OB2

3ob2


Resolution: 2.5→47.05 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.903 / SU B: 11.541 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 0.962 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26397 2448 6.9 %RANDOM
Rwork0.19931 ---
obs0.20375 32828 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.761 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7493 0 7 167 7667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0197686
X-RAY DIFFRACTIONr_bond_other_d00.027305
X-RAY DIFFRACTIONr_angle_refined_deg0.7311.95310383
X-RAY DIFFRACTIONr_angle_other_deg0.509316779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3835907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30423.529374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.682151360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9871552
X-RAY DIFFRACTIONr_chiral_restr0.0430.21102
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028594
X-RAY DIFFRACTIONr_gen_planes_other00.021898
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_it2.1184.6983640
X-RAY DIFFRACTIONr_mcbond_other2.1184.6973639
X-RAY DIFFRACTIONr_mcangle_it3.497.0374543
X-RAY DIFFRACTIONr_mcangle_other3.497.0384544
X-RAY DIFFRACTIONr_scbond_it2.0674.9224046
X-RAY DIFFRACTIONr_scbond_other2.0674.9224046
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5457.2815840
X-RAY DIFFRACTIONr_long_range_B_refined6.11437.769385
X-RAY DIFFRACTIONr_long_range_B_other6.08437.7789349
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å
RfactorNum. reflection% reflection
Rfree0.288 182 7.1 %
Rwork0.298 2366 -
obs--98.91 %

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