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- PDB-26lm: Crystal structure of cblb -

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Basic information

Entry
Database: PDB / ID: 26lm
TitleCrystal structure of cblb
ComponentsE3 ubiquitin-protein ligase CBL-B
KeywordsFLAVOPROTEIN / LSD1
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: 1.95 Å
AuthorsZhiyan, D. / Danyan, C. / Lingyu, S. / Bing, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)82373720 China
CitationJournal: To Be Published
Title: Phage Display-Derived Cyclic Peptides Targeting the TKB Domain of CBLB with T Cell Immunostimulatory Activity
Authors: Lingyu, S. / Danyan, C. / Bing, X. / Yubo, Z.
History
DepositionMay 6, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 17, 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


Theoretical massNumber of molelcules
Total (without water)46,4501
Polymers46,4501
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.840, 71.840, 212.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#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: 46450.211 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium chloride, 0.1 M BICINE pH 9.0, -20% v/v Polyethylene glycol monomethylether 550

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.81→50.8 Å / Num. obs: 77285 / % possible obs: 95.8 % / Redundancy: 20 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.018 / Rrim(I) all: 0.093 / Net I/σ(I): 28
Reflection shellResolution: 1.81→1.9 Å / Redundancy: 15 % / Rmerge(I) obs: 0.084 / Num. unique obs: 2353 / CC1/2: 0.591 / Rpim(I) all: 0.551 / Rrim(I) all: 2.501

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→50.42 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 3742 4.84 %
Rwork0.2116 --
obs0.213 77285 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→50.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 0 0 180 3332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093246
X-RAY DIFFRACTIONf_angle_d1.1684402
X-RAY DIFFRACTIONf_dihedral_angle_d6.447431
X-RAY DIFFRACTIONf_chiral_restr0.063479
X-RAY DIFFRACTIONf_plane_restr0.013566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.30461370.29512696X-RAY DIFFRACTION100
1.98-20.31571370.27942765X-RAY DIFFRACTION100
2-2.030.28631390.27052707X-RAY DIFFRACTION100
2.03-2.060.29131390.2542740X-RAY DIFFRACTION100
2.06-2.090.28441420.24712689X-RAY DIFFRACTION100
2.09-2.120.27651420.24492746X-RAY DIFFRACTION100
2.12-2.160.30241350.242690X-RAY DIFFRACTION100
2.16-2.190.30471410.23812755X-RAY DIFFRACTION100
2.19-2.230.27581400.23432718X-RAY DIFFRACTION100
2.23-2.280.25551340.23482716X-RAY DIFFRACTION100
2.28-2.320.30891360.22672739X-RAY DIFFRACTION100
2.32-2.370.27961420.21862724X-RAY DIFFRACTION100
2.37-2.430.25711400.21662719X-RAY DIFFRACTION100
2.43-2.490.26921400.22012736X-RAY DIFFRACTION100
2.49-2.560.25051400.22682736X-RAY DIFFRACTION100
2.56-2.630.25011350.23172702X-RAY DIFFRACTION100
2.63-2.720.29231360.23512703X-RAY DIFFRACTION100
2.72-2.810.26431430.23462724X-RAY DIFFRACTION100
2.81-2.930.23341390.23322729X-RAY DIFFRACTION100
2.93-3.060.30471340.23092730X-RAY DIFFRACTION100
3.06-3.220.28131390.2282727X-RAY DIFFRACTION100
3.22-3.420.28021390.21262758X-RAY DIFFRACTION100
3.42-3.690.26831340.20282691X-RAY DIFFRACTION100
3.69-4.060.19871380.18532748X-RAY DIFFRACTION100
4.06-4.640.1531340.17352717X-RAY DIFFRACTION100
4.64-5.850.19721420.1912713X-RAY DIFFRACTION100
5.85-50.420.20431450.19532725X-RAY DIFFRACTION100

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