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- PDB-9wgu: Crystal structure of Cbl-b bound to compound -

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Basic information

Entry
Database: PDB / ID: 9wgu
TitleCrystal structure of Cbl-b bound to compound
ComponentsE3 ubiquitin-protein ligase CBL-B
KeywordsSIGNALING PROTEIN / 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: 1.95 Å
AuthorsFan, Y. / Ding, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Cbl-b bound to compound
Authors: Fan, Y. / Ding, X.
History
DepositionAug 25, 2025Deposition site: PDBJ / Processing site: PDBC
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
AAA: E3 ubiquitin-protein ligase CBL-B
BBB: E3 ubiquitin-protein ligase CBL-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,39323
Polymers90,1412
Non-polymers2,25221
Water10,701594
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.655, 102.781, 74.647
Angle α, β, γ (deg.)90.000, 90.246, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AAABBB

#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: 45070.660 Da / Num. of mol.: 2
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 , 5 types, 615 molecules

#2: Chemical ChemComp-A1EWZ / 2-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-7-[[(3~{S})-3-methylpiperidin-1-yl]methyl]-5-(trifluoromethyl)-3,4-dihydroisoquinolin-1-one


Mass: 551.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H36F3N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH7.5, 8% EG, 10% PEG8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.95→49.665 Å / Num. obs: 61298 / % possible obs: 98.5 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.3
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 4315 / CC1/2: 0.656

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→49.665 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.488 / SU ML: 0.123 / Cross valid method: FREE R-VALUE / ESU R: 0.167 / ESU R Free: 0.156
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2256 2954 4.821 %
Rwork0.1739 58318 -
all0.176 --
obs-61272 98.427 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.015 Å20 Å2-0.262 Å2
2--1.151 Å20 Å2
3----1.164 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6249 0 138 594 6981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136604
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156232
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.6788900
X-RAY DIFFRACTIONr_angle_other_deg1.3141.59814386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1385778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07722.216352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.353151168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9481542
X-RAY DIFFRACTIONr_chiral_restr0.0790.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021566
X-RAY DIFFRACTIONr_nbd_refined0.20.21355
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.25722
X-RAY DIFFRACTIONr_nbtor_refined0.170.23252
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2411
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0120.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.218
X-RAY DIFFRACTIONr_nbd_other0.1760.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.217
X-RAY DIFFRACTIONr_mcbond_it2.5463.0833080
X-RAY DIFFRACTIONr_mcbond_other2.5443.0833077
X-RAY DIFFRACTIONr_mcangle_it3.7654.6063842
X-RAY DIFFRACTIONr_mcangle_other3.7664.6073843
X-RAY DIFFRACTIONr_scbond_it3.3693.5293524
X-RAY DIFFRACTIONr_scbond_other3.3693.5293525
X-RAY DIFFRACTIONr_scangle_it5.1865.1195046
X-RAY DIFFRACTIONr_scangle_other5.1855.1195047
X-RAY DIFFRACTIONr_lrange_it7.07236.6767695
X-RAY DIFFRACTIONr_lrange_other7.04136.3557574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.2972100.2694304X-RAY DIFFRACTION99.0129
2.001-2.0550.2852010.2484228X-RAY DIFFRACTION98.8175
2.055-2.1150.282110.2194076X-RAY DIFFRACTION98.8699
2.115-2.180.2472040.2074022X-RAY DIFFRACTION98.8076
2.18-2.2510.2582110.1913770X-RAY DIFFRACTION98.1751
2.251-2.330.2621840.1893700X-RAY DIFFRACTION98.2296
2.33-2.4180.2431870.1783559X-RAY DIFFRACTION98.1399
2.418-2.5170.2081680.1673444X-RAY DIFFRACTION97.7273
2.517-2.6290.2411710.1673283X-RAY DIFFRACTION98.0693
2.629-2.7570.2291680.1723154X-RAY DIFFRACTION98.1388
2.757-2.9060.2551440.1773017X-RAY DIFFRACTION98.3204
2.906-3.0820.2251650.1672832X-RAY DIFFRACTION98.359
3.082-3.2940.21560.1592640X-RAY DIFFRACTION98.2431
3.294-3.5570.1911010.1592573X-RAY DIFFRACTION98.4899
3.557-3.8960.2411010.1662291X-RAY DIFFRACTION98.2744
3.896-4.3540.162980.1412112X-RAY DIFFRACTION98.793
4.354-5.0250.222840.1511837X-RAY DIFFRACTION98.5128
5.025-6.1480.243700.1791586X-RAY DIFFRACTION98.9839
6.148-8.6650.189730.1671217X-RAY DIFFRACTION98.6993
8.665-49.6650.193470.162673X-RAY DIFFRACTION96.7742

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