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- PDB-9i0c: E3 ubiquitin ligase CBL-B in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 9i0c
TitleE3 ubiquitin ligase CBL-B in complex with inhibitor
ComponentsE3 ubiquitin-protein ligase CBL-B
KeywordsLIGASE
Function / homology
Function and homology information


regulation of platelet-derived growth factor receptor-alpha signaling pathway / regulation protein catabolic process at postsynapse / NLS-bearing protein import into nucleus / regulation of postsynaptic neurotransmitter receptor internalization / negative regulation of T cell activation / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of T cell receptor signaling pathway / protein K63-linked ubiquitination / phosphotyrosine residue binding / receptor tyrosine kinase binding ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / regulation protein catabolic process at postsynapse / NLS-bearing protein import into nucleus / regulation of postsynaptic neurotransmitter receptor internalization / negative regulation of T cell activation / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of T cell receptor signaling pathway / protein K63-linked ubiquitination / phosphotyrosine residue binding / receptor tyrosine kinase binding / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell surface receptor signaling pathway / postsynapse / protein stabilization / membrane raft / calcium ion binding / glutamatergic synapse / signal transduction / zinc ion binding / 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 domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / SH2 domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / E3 ubiquitin-protein ligase CBL-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.123 Å
AuthorsSchimpl, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Inhibiting Ubiquitin ligases: A Case Study on the Discovery, Mechanism, and Optimization of Cbl-b Inhibitors
Authors: Chinn, A.J. / Quinn, T.R. / Boerth, J.A. / Kohara, K. / Bommakanti, G.
History
DepositionJan 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,3525
Polymers45,8101
Non-polymers5424
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint3 kcal/mol
Surface area18040 Å2
Unit cell
Length a, b, c (Å)57.183, 74.533, 97.499
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


Mass: 45809.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBLB / Production host: Escherichia coli (E. coli) / References: UniProt: Q13191
#2: Chemical ChemComp-A1IZE / 1-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-5-(trifluoromethyl)pyridin-2-one


Mass: 388.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19F3N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 9 % PEG8000, 0.05 M Mg Acetate, 2.5 % MPD, 0.05 M PCPT pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.12→48.75 Å / Num. obs: 23838 / % possible obs: 97.7 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.035 / Rrim(I) all: 0.127 / Χ2: 0.9 / Net I/σ(I): 13.5 / Num. measured all: 317742
Reflection shellResolution: 2.12→2.17 Å / % possible obs: 74.7 % / Redundancy: 12.3 % / Rmerge(I) obs: 1.517 / Num. measured all: 15922 / Num. unique obs: 1293 / CC1/2: 0.661 / Rpim(I) all: 0.433 / Rrim(I) all: 1.581 / Χ2: 0.59 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (10-JUL-2024)refinement
Aimlessdata scaling
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.123→48.75 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.244 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.198
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 1196 5.04 %RANDOM
Rwork0.2137 ---
obs0.2158 23749 98.2 %-
Displacement parametersBiso mean: 53.65 Å2
Baniso -1Baniso -2Baniso -3
1--7.8219 Å20 Å20 Å2
2--10.9741 Å20 Å2
3----3.1522 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2.123→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3105 0 31 52 3188
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083211HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.864347HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1121SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes538HARMONIC5
X-RAY DIFFRACTIONt_it3211HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion17.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion410SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2642SEMIHARMONIC4
LS refinement shellResolution: 2.123→2.15 Å
RfactorNum. reflection% reflection
Rfree0.4114 -4.63 %
Rwork0.3541 453 -
obs--61.45 %
Refinement TLS params.Method: refined / Origin x: 19.8623 Å / Origin y: 15.6316 Å / Origin z: 28.7004 Å
111213212223313233
T-0.0855 Å20.0365 Å20.0265 Å2--0.1223 Å20.0125 Å2---0.0926 Å2
L0.2636 °2-0.1628 °2-0.2468 °2-1.8789 °2-0.0655 °2--1.1165 °2
S0.1221 Å °0.007 Å °-0.037 Å °-0.0209 Å °-0.0514 Å °0.0468 Å °-0.1587 Å °-0.0612 Å °-0.0707 Å °
Refinement TLS groupSelection details: { A|* }

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