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- PDB-3vgo: Crystal structure of the N-terminal fragment of Cbl-b -

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Basic information

Entry
Database: PDB / ID: 3vgo
TitleCrystal structure of the N-terminal fragment of Cbl-b
ComponentsE3 ubiquitin-protein ligase CBL-B
KeywordsLIGASE / MEROHEDRAL TWINNING / E3 ligase
Function / homology
Function and homology information


regulation of platelet-derived growth factor receptor-alpha signaling pathway / T cell anergy / positive regulation of T cell anergy / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of T cell receptor signaling pathway / NLS-bearing protein import into nucleus / phosphotyrosine residue binding / positive regulation of protein ubiquitination / protein catabolic process ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / T cell anergy / positive regulation of T cell anergy / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of T cell receptor signaling pathway / NLS-bearing protein import into nucleus / phosphotyrosine residue binding / positive regulation of protein ubiquitination / protein catabolic process / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / SH3 domain binding / positive regulation of protein catabolic process / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / T cell receptor signaling pathway / protein ubiquitination / intracellular signal transduction / immune response / membrane raft / calcium ion binding / signal transduction / zinc ion binding / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Prokaryotic RING finger family 4 / E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / 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 ...Prokaryotic RING finger family 4 / E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / 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 / 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 / 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-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKobashigawa, Y. / Noda, N.N. / Inagaki, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Autoinhibition and phosphorylation-induced activation mechanisms of human cancer and autoimmune disease-related E3 protein Cbl-b
Authors: Kobashigawa, Y. / Tomitaka, A. / Kumeta, H. / Noda, N.N. / Yamaguchi, M. / Inagaki, F.
History
DepositionAug 18, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)136,9153
Polymers136,9153
Non-polymers00
Water0
1
A: E3 ubiquitin-protein ligase CBL-B


Theoretical massNumber of molelcules
Total (without water)45,6381
Polymers45,6381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase CBL-B


Theoretical massNumber of molelcules
Total (without water)45,6381
Polymers45,6381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: E3 ubiquitin-protein ligase CBL-B


Theoretical massNumber of molelcules
Total (without water)45,6381
Polymers45,6381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.876, 98.876, 105.182
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein E3 ubiquitin-protein ligase CBL-B


Mass: 45638.297 Da / Num. of mol.: 3 / Fragment: N-terminal fragment, UNP residues 39-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBLB / Plasmid: pGBHPS / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta (DE3)
References: UniProt: Q13191, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 25% PEG 3350, 0.1M bicine, 0.8M KNO3, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
merohedral11H, K, L10.5
merohedral11h+k,-k,-l20.5
ReflectionResolution: 3→50 Å / Num. all: 23182 / Num. obs: 23066 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 11.9
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.525 / % possible all: 90.2

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1pfv

1pfv


Resolution: 3.1→42.82 Å / Data cutoff high absF: 57063.23 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED. CNS script refine_twin.inp was used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.328 1909 9.4 %CNS SCRIPT MAKE_CV_TWIN.INP, ENSURES THAT TWIN-RELATED PAIRS OF REFLECTIONS ARE EITHER BOTH IN TEST OR BOTH IN WORK SET
Rwork0.27 ---
all0.276 20849 --
obs0.27 20286 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.1978 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 52.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2---0.76 Å20 Å2
3---1.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.74 Å0.65 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 3.1→42.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6668 0 0 0 6668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.21 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.318 156 8.1 %
Rwork0.335 1769 -
obs-1925 92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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