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- PDB-2ooa: crystal structure of the UBA domain from Cbl-b ubiquitin ligase -

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Basic information

Entry
Database: PDB / ID: 2ooa
Titlecrystal structure of the UBA domain from Cbl-b ubiquitin ligase
ComponentsE3 ubiquitin-protein ligase CBL-B
KeywordsLIGASE / alpha-helical domain
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
E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / 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. ...E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / 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 / Ubiquitin-associated (UBA) domain / Ubiquitin associated domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Helicase, Ruva Protein; domain 3 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CBL-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.56 Å
AuthorsKozlov, G. / Gehring, K.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural basis for ubiquitin-mediated dimerization and activation of the ubiquitin protein ligase Cbl-b.
Authors: Peschard, P. / Kozlov, G. / Lin, T. / Mirza, I.A. / Berghuis, A.M. / Lipkowitz, S. / Park, M. / Gehring, K.
History
DepositionJan 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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


Theoretical massNumber of molelcules
Total (without water)11,4072
Polymers11,4072
Non-polymers00
Water2,342130
1
A: E3 ubiquitin-protein ligase CBL-B


Theoretical massNumber of molelcules
Total (without water)5,7031
Polymers5,7031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase CBL-B


Theoretical massNumber of molelcules
Total (without water)5,7031
Polymers5,7031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.138, 50.199, 78.343
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-B / Signal transduction protein CBL-B / SH3-binding protein CBL-B / Casitas B-lineage lymphoma proto- ...Signal transduction protein CBL-B / SH3-binding protein CBL-B / Casitas B-lineage lymphoma proto-oncogene b / RING finger protein 56


Mass: 5703.276 Da / Num. of mol.: 2 / Fragment: UBA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBLB, RNF56 / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q13191, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 1.2M sodium/potassium phosphate, 12% glycerol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 28, 2005 / Details: mirrors
RadiationMonochromator: Si (111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. all: 13332 / Num. obs: 13003 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 29.2
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 7.4 / Num. unique all: 883 / % possible all: 89.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.56→17.29 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.11 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23992 631 4.9 %RANDOM
Rwork0.2043 ---
all0.206 13332 --
obs0.206 12372 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.835 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.56→17.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms666 0 0 130 796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022674
X-RAY DIFFRACTIONr_angle_refined_deg1.261.975904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.993582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.9924.11834
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77715124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.025156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2100
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02512
X-RAY DIFFRACTIONr_nbd_refined0.2140.2338
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2479
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0890.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.26
X-RAY DIFFRACTIONr_mcbond_it0.6541.5429
X-RAY DIFFRACTIONr_mcangle_it0.9642664
X-RAY DIFFRACTIONr_scbond_it1.8463268
X-RAY DIFFRACTIONr_scangle_it3.0744.5240
LS refinement shellResolution: 1.56→1.598 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 33 -
Rwork0.239 883 -
obs--96.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7781-0.65150.94773.54291.77186.19140.255-0.1727-0.1080.2004-0.2438-0.02060.595-0.2417-0.01120.1011-0.0279-0.00010.03140.01180.01181.137411.1375-4.1713
22.2287-0.13321.34414.88711.33337.80240.0412-0.1766-0.03250.0383-0.01340.15170.238-0.3143-0.02780.0428-0.02010.01320.06620.01940.0498-2.596613.8412-11.1272
30.5317-0.79090.05524.88340.71752.3973-0.0716-0.05250.0649-0.07630.205-0.3655-0.00540.1839-0.13350.01580.01740.01030.0422-0.01970.06633.93619.3399-14.6693
47.2566-0.6913-0.33524.2185-2.54156.84840.0680.2354-0.1583-0.3199-0.02590.10960.8053-0.1248-0.04210.1254-0.0323-0.01340.024-0.01680.0084-6.061310.02735.423
51.9861-0.6012.26573.3549-1.96849.4140.12950.1072-0.0145-0.0462-0.0841-0.08130.43820.379-0.04540.05770.01960.0050.0429-0.01410.0504-0.376112.396911.2227
60.85341.1293-0.26796.6903-0.38522.16-0.0855-0.08360.12710.1670.11470.3495-0.0411-0.339-0.02930.0107-0.00580.00390.0578-0.00820.0661-5.658219.417216.1521
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA932 - 94311 - 22
2X-RAY DIFFRACTION2AA944 - 96123 - 40
3X-RAY DIFFRACTION3AA962 - 97341 - 52
4X-RAY DIFFRACTION4BB932 - 94311 - 22
5X-RAY DIFFRACTION5BB944 - 96323 - 42
6X-RAY DIFFRACTION6BB964 - 97343 - 52

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