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- PDB-2y1m: Structure of native c-Cbl -

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Basic information

Entry
Database: PDB / ID: 2y1m
TitleStructure of native c-Cbl
ComponentsE3 UBIQUITIN-PROTEIN LIGASE
KeywordsLIGASE / UBIQUITIN RING E3 LIGASE
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 / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / Regulation of KIT signaling / positive regulation of epidermal growth factor receptor signaling pathway / Interleukin-6 signaling / mast cell degranulation / response to starvation ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / Regulation of KIT signaling / positive regulation of epidermal growth factor receptor signaling pathway / Interleukin-6 signaling / mast cell degranulation / response to starvation / response to testosterone / negative regulation of epidermal growth factor receptor signaling pathway / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / protein autoubiquitination / ephrin receptor binding / cellular response to platelet-derived growth factor stimulus / phosphotyrosine residue binding / FLT3 signaling by CBL mutants / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / InlB-mediated entry of Listeria monocytogenes into host cell / response to activity / response to gamma radiation / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / EGFR downregulation / Spry regulation of FGF signaling / Negative regulation of MET activity / Constitutive Signaling by EGFRvIII / cellular response to nerve growth factor stimulus / receptor tyrosine kinase binding / RING-type E3 ubiquitin transferase / positive regulation of receptor-mediated endocytosis / SH3 domain binding / male gonad development / protein polyubiquitination / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / growth cone / ubiquitin-dependent protein catabolic process / response to ethanol / cellular response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cilium / cadherin binding / membrane raft / focal adhesion / calcium ion binding / DNA damage response / symbiont entry into host cell / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / zinc ion binding / plasma membrane / cytosol
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. / Prokaryotic RING finger family 4 / 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 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsDou, H. / Sibbet, G.J. / Huang, D.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural Basis for Autoinhibition and Phosphorylation-Dependent Activation of C-Cbl.
Authors: Dou, H. / Buetow, L. / Hock, A. / Sibbet, G.J. / Vousden, K.H. / Huang, D.T.
History
DepositionDec 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Feb 15, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE
B: E3 UBIQUITIN-PROTEIN LIGASE
C: E3 UBIQUITIN-PROTEIN LIGASE
D: E3 UBIQUITIN-PROTEIN LIGASE
E: E3 UBIQUITIN-PROTEIN LIGASE
F: E3 UBIQUITIN-PROTEIN LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,59824
Polymers269,5726
Non-polymers1,02518
Water2,180121
1
A: E3 UBIQUITIN-PROTEIN LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1004
Polymers44,9291
Non-polymers1713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 UBIQUITIN-PROTEIN LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1004
Polymers44,9291
Non-polymers1713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: E3 UBIQUITIN-PROTEIN LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1004
Polymers44,9291
Non-polymers1713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: E3 UBIQUITIN-PROTEIN LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1004
Polymers44,9291
Non-polymers1713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: E3 UBIQUITIN-PROTEIN LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1004
Polymers44,9291
Non-polymers1713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: E3 UBIQUITIN-PROTEIN LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1004
Polymers44,9291
Non-polymers1713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.800, 148.560, 348.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
E3 UBIQUITIN-PROTEIN LIGASE / CBL C-CBL / CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE / PROTO-ONCOGENE C-CBL / RING FINGER PROTEIN ...CBL C-CBL / CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE / PROTO-ONCOGENE C-CBL / RING FINGER PROTEIN 55 / SIGNAL TRANSDUCTION PROTEIN CBL


Mass: 44928.695 Da / Num. of mol.: 6 / Fragment: RESIDUES 47-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / 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)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.52 Å3/Da / Density % sol: 65.04 % / Description: NONE
Crystal growpH: 9
Details: 0.1 M TRIS-HCL, PH 9.0-9.5, 3.7-4.0 M SODIUM FORMATE, 5 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9395
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2010
RadiationMonochromator: SYNCHROTRON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 104817 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 49.02 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11
Reflection shellResolution: 2.67→2.81 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.4 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B47

1b47


Resolution: 2.67→47.615 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 29.44 / Stereochemistry target values: ML
Details: FOLLOWING RESIDUES WERE NOT BUILT DUE TO POORLY DEFINED ELECTRON DENSITY.CHAIN A RESIDUES 354-358 CHAIN B RESIDUES 356-359, CHAIN C RESIDUES 355-358, CHAIN D RESIDUES 355-358, CHAIN E ...Details: FOLLOWING RESIDUES WERE NOT BUILT DUE TO POORLY DEFINED ELECTRON DENSITY.CHAIN A RESIDUES 354-358 CHAIN B RESIDUES 356-359, CHAIN C RESIDUES 355-358, CHAIN D RESIDUES 355-358, CHAIN E RESIDUES 354-359 AND CHAIN F RESIDUES 354-358. GLU354 AND ASP359 IN CHAIN C WERE BUILT AS ALANINES DUE TO POORLY DEFINED ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.2629 5103 5 %
Rwork0.2184 --
obs0.2206 101826 94.45 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.901 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso mean: 57.18 Å2
Baniso -1Baniso -2Baniso -3
1--8.5788 Å2-0 Å20 Å2
2---11.1607 Å20 Å2
3---19.7395 Å2
Refinement stepCycle: LAST / Resolution: 2.67→47.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18693 0 18 121 18832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01119168
X-RAY DIFFRACTIONf_angle_d1.3525885
X-RAY DIFFRACTIONf_dihedral_angle_d18.1277203
X-RAY DIFFRACTIONf_chiral_restr0.0842774
X-RAY DIFFRACTIONf_plane_restr0.0073306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.76540.414770.3458687X-RAY DIFFRACTION86
2.7654-2.87610.37574710.31449114X-RAY DIFFRACTION90
2.8761-3.0070.34064960.28489489X-RAY DIFFRACTION93
3.007-3.16550.3375070.27249679X-RAY DIFFRACTION95
3.1655-3.36380.30615120.24729891X-RAY DIFFRACTION97
3.3638-3.62340.25434910.21669974X-RAY DIFFRACTION98
3.6234-3.98790.24025090.19669999X-RAY DIFFRACTION98
3.9879-4.56460.21995410.17710023X-RAY DIFFRACTION98
4.5646-5.74930.22315300.19059976X-RAY DIFFRACTION97
5.7493-47.62230.23685690.19859891X-RAY DIFFRACTION94

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