[English] 日本語
Yorodumi
- PDB-10ys: Structure of Cbl-B bound to compound 33 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 10ys
TitleStructure of Cbl-B bound to compound 33
ComponentsE3 ubiquitin-protein ligase CBL-B
KeywordsLIGASE / Ubiquitin ligase / E3 / inhibitor
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
: / IODIDE ION / E3 ubiquitin-protein ligase CBL-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 Leading to a Potent and Selective Cbl‐b Inactive-State Inhibitor That Demonstrated In Vivo Efficacy.
Authors: Liang, J. / Lambrecht, M.J. / Huestis, M.P. / Zhu, B. / Barton, L.M. / Castanedo, G.M. / Ung, P.M. / Larouche-Gauthier, R. / Jakalian, A. / Leclerc, J.P. / Yadav, A. / Haghshenas, P. / ...Authors: Liang, J. / Lambrecht, M.J. / Huestis, M.P. / Zhu, B. / Barton, L.M. / Castanedo, G.M. / Ung, P.M. / Larouche-Gauthier, R. / Jakalian, A. / Leclerc, J.P. / Yadav, A. / Haghshenas, P. / Aubert-Nicol, S. / Ismaili, H. / Zhao, L. / Leblanc, M. / de Almeida, H. / Wang, Q. / Garner, T. / Tan, S. / Prangley, M.S. / Pang, J. / Murray, J.M. / Yu, C. / Hsu, P.L. / Rutz, S. / Ishizuka, I. / Huang, H. / Gao, C. / Chen, M. / Mutter-Rottmayer, L. / Kakiuchi-Kiyota, S. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,59025
Polymers95,5452
Non-polymers3,04523
Water1,838102
1
A: E3 ubiquitin-protein ligase CBL-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,51014
Polymers47,7731
Non-polymers1,73713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase CBL-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,08011
Polymers47,7731
Non-polymers1,30810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.275, 74.032, 106.800
Angle α, β, γ (deg.)90.00, 93.68, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#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.: 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

-
Non-polymers , 8 types, 125 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-A1DCD / 2-{3-[(1r,3r)-3-methoxy-1-(4-methyl-4H-1,2,4-triazol-3-yl)cyclobutyl]phenyl}-6-{[(1-methylcyclobutyl)amino]methyl}-4-(trifluoromethyl)-2,3-dihydro-1H-isoindol-1-one


Mass: 539.592 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H32F3N5O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 12% PEG4000, 0.1M Tris pH8.5, 0.1M NaI

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→60.8 Å / Num. obs: 20402 / % possible obs: 90.9 % / Redundancy: 2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.14 / Net I/σ(I): 4.3
Reflection shellResolution: 2.3→2.43 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 130 / CC1/2: 0.53

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→60.8 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 1002 4.91 %
Rwork0.2071 --
obs0.2099 20402 51.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→60.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6267 0 118 102 6487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0016571
X-RAY DIFFRACTIONf_angle_d0.48897
X-RAY DIFFRACTIONf_dihedral_angle_d12.8842521
X-RAY DIFFRACTIONf_chiral_restr0.037941
X-RAY DIFFRACTIONf_plane_restr0.0031128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID
2.3-2.430.450570.2709123X-RAY DIFFRACTION
2.43-2.580.458180.3027382X-RAY DIFFRACTION
2.58-2.780.3304660.2858914X-RAY DIFFRACTION
2.78-3.060.28481300.28382575X-RAY DIFFRACTION
3.06-3.50.30822250.24124594X-RAY DIFFRACTION
3.5-4.410.26492820.19115368X-RAY DIFFRACTION
4.41-100.22452740.17745444X-RAY DIFFRACTION
Refinement TLS params.Method: refined / Origin x: 12.0791 Å / Origin y: 14.3582 Å / Origin z: 25.5407 Å
111213212223313233
T0.2283 Å20.0934 Å2-0.0398 Å2-0.139 Å20.0096 Å2--0.2052 Å2
L0.1534 °20.1634 °2-0.5756 °2--0.1182 °20.016 °2--0.7146 °2
S0.039 Å °0.0302 Å °0.0122 Å °0.0714 Å °-0.013 Å °-0.0302 Å °0.0023 Å °-0.0924 Å °-0.0187 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more