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- PDB-9xzd: E3 ubiquitin-protein ligase CBL-B in complex with compound 8 -

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Basic information

Entry
Database: PDB / ID: 9xzd
TitleE3 ubiquitin-protein ligase CBL-B in complex with compound 8
ComponentsE3 ubiquitin-protein ligase CBL-B
KeywordsLIGASE / E3 ubiquitin-protein ligase
Function / homology
Function and homology information


regulation of platelet-derived growth factor receptor-alpha signaling pathway / NLS-bearing protein import into nucleus / 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 ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / NLS-bearing protein import into nucleus / 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 / protein stabilization / membrane raft / calcium ion binding / 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: 1.65 Å
AuthorsGajewski, S. / Clifton, M.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Discovery and characterization of Cbl-b intra-molecular inhibitory glues with biological activity.
Authors: Gajewski, S.
History
DepositionAug 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 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)46,4179
Polymers45,4581
Non-polymers9598
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.950, 71.240, 116.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 45458.008 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, 235 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-XLH / N-(3-{(1S)-1-[(4-methyl-4H-1,2,4-triazol-3-yl)sulfanyl]ethyl}phenyl)-6-(trifluoromethyl)pyridine-2-carboxamide


Mass: 407.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16F3N5OS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES pH 5.6-6.2, 200 mM LiSO4, 16-20% PEG 3350, 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→44.99 Å / Num. obs: 49956 / % possible obs: 98.61 % / Redundancy: 8.1 % / Biso Wilson estimate: 23.12 Å2 / Rpim(I) all: 0.04053 / Net I/σ(I): 13.06
Reflection shellResolution: 1.65→1.709 Å / Num. unique obs: 4891 / Rpim(I) all: 0.6631

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→44.99 Å / SU ML: 0.2571 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.5707
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2221 2000 4 %
Rwork0.1977 47956 -
obs0.1986 49956 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.2 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2965 0 52 227 3244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01343140
X-RAY DIFFRACTIONf_angle_d1.19544277
X-RAY DIFFRACTIONf_chiral_restr0.0706463
X-RAY DIFFRACTIONf_plane_restr0.012545
X-RAY DIFFRACTIONf_dihedral_angle_d12.80151124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.37371390.38133337X-RAY DIFFRACTION97.61
1.69-1.740.37921410.33813364X-RAY DIFFRACTION97.44
1.74-1.790.30961390.29363338X-RAY DIFFRACTION97.29
1.79-1.850.31661400.25123348X-RAY DIFFRACTION98.03
1.85-1.910.23241410.21153385X-RAY DIFFRACTION98.3
1.91-1.990.21391400.20553378X-RAY DIFFRACTION98.41
1.99-2.080.24721410.21843382X-RAY DIFFRACTION98.27
2.08-2.190.25231420.21643398X-RAY DIFFRACTION98.83
2.19-2.330.20581420.18443421X-RAY DIFFRACTION99.14
2.33-2.50.2181450.18443444X-RAY DIFFRACTION98.79
2.51-2.760.23251440.19673462X-RAY DIFFRACTION99.61
2.76-3.160.23431440.20093480X-RAY DIFFRACTION99.26
3.16-3.970.19871480.17033525X-RAY DIFFRACTION99.51
3.98-44.990.17961540.17243694X-RAY DIFFRACTION99.74
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)
11.83655595569-0.5467420244010.9527422853930.955461407559-0.3963321040222.68324661776-0.2824431977840.08238885997460.3832609520770.09248715619170.0559705960077-0.0401753271737-0.734652285625-0.08355592808330.01250753184060.3208690352580.0119607962214-0.04417566840190.1009062641450.05132523528950.2238386937486.132977754946.59098063691-16.7022359997
21.381879592990.880873648348-0.01385593219762.338913801-0.2219342174191.34022387965-0.02677223905040.037493374527-0.01751203730980.0823201276150.0212507955177-0.00164880262047-0.001296045983790.0462678157439-0.005161783798540.07490676330770.007823839627910.0018644618030.1338506172840.001750308264150.085527176967411.034589904-17.4597390728-8.08541874522
30.6798860634320.77129150531-0.4235284695060.60440010598-0.4843587652260.125375817326-0.2417656982461.49777492590.54996234791-0.1882878794860.6187521362760.07409617982130.00758478874417-1.1192521625-0.1340637486790.305607909428-0.07630623152830.07775011798630.7732803439830.1740878059280.3153724075120.635076425-1.79182546739-35.9954980466
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 38 through 239 )38 - 2391 - 198
22chain 'A' and (resid 240 through 356 )240 - 356199 - 311
33chain 'A' and (resid 357 through 426 )357 - 426312 - 381

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