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- PDB-10zj: Structure of Cbl-B bound to compound 8 -

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Basic information

Entry
Database: PDB / ID: 10zj
TitleStructure of Cbl-B bound to compound 8
ComponentsE3 ubiquitin-protein ligase CBL-B
KeywordsLIGASE/INHIBITOR / Ubiquitin ligase / E3 / inhibitor / LIGASE / LIGASE-INHIBITOR complex
Function / homology
Function and homology information


regulation of platelet-derived growth factor receptor-alpha signaling pathway / T cell anergy / regulation protein catabolic process at postsynapse / positive regulation of T cell anergy / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / 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 ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / T cell anergy / regulation protein catabolic process at postsynapse / positive regulation of T cell anergy / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / 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 / positive regulation of protein ubiquitination / protein catabolic process / receptor tyrosine kinase binding / RING-type E3 ubiquitin transferase / positive regulation of protein catabolic process / ubiquitin protein ligase activity / T cell receptor signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / protein stabilization / intracellular signal transduction / postsynapse / immune response / membrane raft / calcium ion binding / glutamatergic synapse / 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 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: 1.77 Å
AuthorsMurray, J. / Yu, C. / Hsu, P.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2026
Title: Optimization and In Vivo Characterization of a Series of Cbl‐b Inactive-State Inhibitors.
Authors: Lambrecht, M.J. / Liang, J. / Ung, P.M. / Huestis, M.P. / Zhu, B.Y. / Barton, L.M. / Castanedo, G.M. / Zbieg, J.R. / Larouche-Gauthier, R. / Jakalian, A. / Leclerc, J.P. / Yadav, A. / ...Authors: Lambrecht, M.J. / Liang, J. / Ung, P.M. / Huestis, M.P. / Zhu, B.Y. / Barton, L.M. / Castanedo, G.M. / Zbieg, J.R. / Larouche-Gauthier, R. / Jakalian, A. / Leclerc, J.P. / Yadav, A. / Haghshenas, P. / Aubert-Nicol, S. / Ismaili, H. / Zhao, L. / Leblanc, M. / Wang, J. / Wang, S. / Wang, Q. / Garner, T. / Tan, S. / Prangley, M. / Broccatelli, F. / Pang, J. / Murray, J. / Yu, C. / Hsu, P. / Rutz, S. / Kakiuchi-Kiyota, S. / Ishizuka, I. / Leung, D.H. / Kou, P. / Bao, L. / Wang, X.
History
DepositionFeb 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6357
Polymers47,7731
Non-polymers8636
Water5,585310
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.190, 74.120, 97.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein E3 ubiquitin-protein ligase CBL-B / Casitas B-lineage lymphoma proto-oncogene b / RING finger protein 56 / RING-type E3 ubiquitin ...Casitas B-lineage lymphoma proto-oncogene b / RING finger protein 56 / RING-type E3 ubiquitin transferase CBL-B / SH3-binding protein CBL-B / Signal transduction protein CBL-B


Mass: 47772.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBLB, RNF56, Nbla00127 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13191, RING-type E3 ubiquitin transferase

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Non-polymers , 6 types, 316 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-A1DCC / 6-{[(3,3-difluoropropyl)amino]methyl}-2-(3-{3-[(R)-fluoro(4-methyl-4H-1,2,4-triazol-3-yl)methyl]oxetan-3-yl}phenyl)-4-(trifluoromethyl)-2,3-dihydro-1H-isoindol-1-one


Mass: 553.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25F6N5O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.01M MgCl2, 10% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→49.29 Å / Num. obs: 32919 / % possible obs: 95.3 % / Redundancy: 2 % / CC1/2: 0.99 / Net I/σ(I): 11.5
Reflection shellResolution: 1.77→1.83 Å / Num. unique obs: 902 / CC1/2: 0.62

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Processing

Software
NameVersionClassification
PHENIX1.19-4092_finalrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→49.29 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2688 1575 4.78 %
Rwork0.2248 --
obs0.2269 32919 80.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3172 0 52 310 3534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013344
X-RAY DIFFRACTIONf_angle_d0.3994535
X-RAY DIFFRACTIONf_dihedral_angle_d11.9121258
X-RAY DIFFRACTIONf_chiral_restr0.038481
X-RAY DIFFRACTIONf_plane_restr0.003579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.830.241645857X-RAY DIFFRACTION25
1.83-1.890.3162610.29331083X-RAY DIFFRACTION31
1.89-1.970.3686920.34661774X-RAY DIFFRACTION51
1.97-2.060.32131060.29242753X-RAY DIFFRACTION78
2.06-2.170.29891580.27393375X-RAY DIFFRACTION96
2.17-2.30.37861940.30173504X-RAY DIFFRACTION100
2.3-2.480.26411570.24973552X-RAY DIFFRACTION100
2.48-2.730.2621950.24253538X-RAY DIFFRACTION100
2.73-3.120.27581820.23313564X-RAY DIFFRACTION100
3.12-3.940.24881760.19613593X-RAY DIFFRACTION100
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)
10.14440.20040.32780.84830.65381.0454-0.23420.01510.1695-0.36350.3425-0.7811-0.17510.79810.12570.2540.22990.03060.348-0.05530.347827.9833-21.2037-29.1947
22.6319-0.8872-1.20042.52540.6721.73660.23050.1003-0.0478-0.1032-0.0226-0.33630.53960.33510.18040.11310.10510.0110.1373-0.02370.153818.478-21.7868-26.4888
30.55850.04940.10922.2869-0.81281.28950.0513-0.03160.00880.00550.01740.13540.0699-0.0381-00.12220.0171-0.01470.1515-0.00240.1335-0.5799-16.9205-19.778
40.59960.356-0.17110.40750.20620.675-0.10080.19750.1630.09490.22690.5964-0.1309-0.2977-0.00170.27340.0530.0790.36410.07380.383-13.3949-18.0623-10.7037
51.28690.65130.37480.6008-0.381.3788-0.0027-0.0555-0.03190.0867-0.0286-0.1515-0.15010.088-0.00010.1604-0.0039-0.02660.1708-0.02730.183214.71712.9236-10.7238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 175 )
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 315 )
4X-RAY DIFFRACTION4chain 'A' and (resid 316 through 356 )
5X-RAY DIFFRACTION5chain 'A' and (resid 357 through 427 )

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