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- PDB-9erz: Structure of CBL-TKBD bound to Ubiquitin-fused CBLock peptide -

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Basic information

Entry
Database: PDB / ID: 9erz
TitleStructure of CBL-TKBD bound to Ubiquitin-fused CBLock peptide
Components
  • E3 ubiquitin-protein ligase CBL
  • Polyubiquitin-C,Ub-fused CBLock peptide
KeywordsLIGASE / Ubiquitin ligase / CBL / peptide inhibitor
Function / homology
Function and homology information


regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / Interleukin-6 signaling / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / response to starvation ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / Interleukin-6 signaling / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / response to starvation / negative regulation of epidermal growth factor receptor signaling pathway / response to testosterone / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / protein autoubiquitination / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / phosphotyrosine residue binding / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / response to activity / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / response to gamma radiation / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling
Similarity search - Function
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 ...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 / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / UBA-like superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / EF-hand domain pair / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / E3 ubiquitin-protein ligase CBL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsAhmed, S.F. / Huang, D.T.
Funding support United Kingdom, European Union, 2items
OrganizationGrant numberCountry
Cancer Research UKA23278 United Kingdom
European Research Council (ERC)647849European Union
CitationJournal: Mol.Ther. / Year: 2025
Title: Locking CBL TKBD in its native conformation presents a novel therapeutic opportunity in mutant CBL-dependent leukemia.
Authors: Ahmed, S.F. / Anand, J. / Zhang, W. / Buetow, L. / Rishi, L. / Mitchell, L. / Bohlen, J. / Lilla, S. / Sibbet, G.J. / Nixon, C. / Patel, A. / Majorek, K.A. / Zanivan, S. / Bustamante, J.C. / ...Authors: Ahmed, S.F. / Anand, J. / Zhang, W. / Buetow, L. / Rishi, L. / Mitchell, L. / Bohlen, J. / Lilla, S. / Sibbet, G.J. / Nixon, C. / Patel, A. / Majorek, K.A. / Zanivan, S. / Bustamante, J.C. / Sidhu, S.S. / Blyth, K. / Huang, D.T.
History
DepositionMar 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: 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: Polyubiquitin-C,Ub-fused CBLock peptide
C: E3 ubiquitin-protein ligase CBL
D: Polyubiquitin-C,Ub-fused CBLock peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2676
Polymers96,1874
Non-polymers802
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, Pulldown method was used to verify the complex in cells
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.783, 87.324, 84.353
Angle α, β, γ (deg.)90.00, 99.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein E3 ubiquitin-protein ligase CBL / Casitas B-lineage lymphoma proto-oncogene / Proto-oncogene c-Cbl / RING finger protein 55 / RING- ...Casitas B-lineage lymphoma proto-oncogene / Proto-oncogene c-Cbl / RING finger protein 55 / RING-type E3 ubiquitin transferase CBL / Signal transduction protein CBL


Mass: 36016.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CBL residues 47-355. N-terminal GS resulted from TEV cleavage
Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 / Production host: Homo sapiens (human) / Strain (production host): BL21(DE3) / Variant (production host): E. coli
References: UniProt: P22681, RING-type E3 ubiquitin transferase
#2: Protein Polyubiquitin-C,Ub-fused CBLock peptide


Mass: 12076.634 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Ub residue 1-74 fused to AAPGGS linker connected to a peptide,Ub residue 1-74 fused to AAPGGS linker connected to a peptide
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Homo sapiens (human) / Strain (production host): BL21(DE3) / Variant (production host): E. coli / References: UniProt: P0CG48
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris Propane, pH 6.0, 0.2 M sodium fluoride, and 20% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.02→60.245 Å / Num. obs: 54602 / % possible obs: 97.2 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Net I/σ(I): 17.1
Reflection shellResolution: 2.02→2.05 Å / Num. unique obs: 2782 / CC1/2: 0.835

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→60.2 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 2676 4.9 %
Rwork0.1781 --
obs0.1806 54602 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→60.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6043 0 2 349 6394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076211
X-RAY DIFFRACTIONf_angle_d0.7688454
X-RAY DIFFRACTIONf_dihedral_angle_d16.9853669
X-RAY DIFFRACTIONf_chiral_restr0.05954
X-RAY DIFFRACTIONf_plane_restr0.0051086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.05570.30671350.25422785X-RAY DIFFRACTION100
2.0557-2.09530.2909780.24472060X-RAY DIFFRACTION73
2.0953-2.1380.26351510.21972839X-RAY DIFFRACTION100
2.138-2.18450.27791220.20552762X-RAY DIFFRACTION100
2.1845-2.23530.2581430.20642806X-RAY DIFFRACTION100
2.2353-2.29120.23141130.20472274X-RAY DIFFRACTION81
2.2912-2.35320.24781500.19992794X-RAY DIFFRACTION100
2.3532-2.42240.29121530.1962782X-RAY DIFFRACTION100
2.4224-2.50060.26261370.20182805X-RAY DIFFRACTION100
2.5006-2.590.27681410.19692817X-RAY DIFFRACTION100
2.59-2.69370.27271500.19882779X-RAY DIFFRACTION100
2.6937-2.81630.2741700.2012773X-RAY DIFFRACTION99
2.8163-2.96480.25831650.20042772X-RAY DIFFRACTION100
2.9648-3.15050.24611380.19562814X-RAY DIFFRACTION99
3.1505-3.39380.22891570.18092789X-RAY DIFFRACTION99
3.3938-3.73520.1931430.16422800X-RAY DIFFRACTION99
3.7352-4.27560.20021380.15012805X-RAY DIFFRACTION99
4.2756-5.38630.21891340.14652827X-RAY DIFFRACTION99
5.3863-60.20.18871580.16822843X-RAY DIFFRACTION99
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)
12.7409-0.45540.33723.2659-0.13573.78290.1691.0098-0.1864-0.7167-0.13760.288-0.052-0.13250.00120.51990.0421-0.05330.8407-0.10590.351770.516912.5243155.7807
22.1309-7.0875-0.68935.06111.04433.79210.21550.8330.1281-0.7019-0.3219-0.434-0.09980.07780.14380.50170.00880.07770.7383-0.00530.636281.967213.4752157.252
32.44580.45040.36663.38881.5654.0377-0.03830.54990.3611-0.187-0.08030.0861-0.3508-0.32140.12880.3550.07140.0160.46650.08480.267374.726623.3662169.4131
41.63420.02360.42492.2677-1.12482.96990.04790.1638-0.03280.039-0.07660.0399-0.1706-0.08550.01140.2180.03570.04240.2774-0.05380.296978.872414.2676185.4172
59.45036.4214.8844.9874.18423.7170.2568-0.3045-0.18381.2125-0.8199-0.07620.21810.8430.55210.63260.0079-0.05550.49680.10260.454776.9523-9.0821219.3924
65.90933.4548-1.5385.95472.7863.850.4034-0.1641-0.1305-1.1307-0.2255-0.1505-0.5529-0.7515-0.13270.61320.0845-0.16510.38630.06750.517873.8482-9.6115211.2496
73.48595.39990.78258.8812.88835.7487-0.2532-0.45220.58620.5104-0.2186-0.4012-0.28060.57760.4560.8017-0.1752-0.20730.851-0.07820.506884.1468-1.1319222.8957
85.4106-0.0009-1.08827.9639-1.41258.8111-0.33890.109-0.05290.06460.02870.0925-0.60650.5250.31870.3994-0.0846-0.04080.31890.00240.470177.4456-0.1619211.6809
98.709-3.15890.1076.59732.31111.0132-0.0835-0.38161.19491.6982-0.02370.278-1.40340.7820.15170.9665-0.2329-0.00590.478-0.08890.549677.17534.9398222.2213
102.0378-1.04912.10972.6882-4.69988.26870.1967-0.89420.01510.42930.41280.80360.1061-0.4152-0.56090.70520.00960.05670.59260.09520.527972.6925-4.7517220.3875
113.34543.76783.82914.24114.30724.3741-0.4582-0.82050.59520.9643-0.38441.2634-0.9972-0.94780.89810.51280.040.11260.413-0.07830.563359.91678.0689193.4893
124.22110.5579-1.4854.3081-1.01368.57180.14450.3034-0.2227-0.11920.38410.10560.1865-0.0446-0.60170.2229-0.01030.01320.365-0.05110.375365.89112.9406182.5423
132.4328-1.25470.44343.5582-0.59341.2704-0.1247-0.2336-0.37070.46290.1003-0.08480.11240.08110.03180.2910.00530.0080.22750.00810.3051103.80763.2991208.2208
143.1131-2.01970.36632.9763-0.49393.27720.11920.547-0.0704-0.2775-0.1361-0.1461-0.03030.08240.02870.215-0.03410.03920.3347-0.020.2773101.693310.7571183.0449
155.90092.34982.76665.6622-1.36492.59290.0674-0.3074-0.3443-0.10250.22550.69980.2359-0.2472-0.24310.84690.18940.03621.15630.04290.9094100.570418.14157.4814
161.6278-2.30391.72495.673-4.49917.2548-0.68520.69121.2517-0.62970.12610.0113-0.06290.41340.50941.21620.0654-0.04091.11650.39491.1786106.117126.2555155.1208
172.37331.42542.07555.14483.99023.5708-1.11261.14051.198-0.8899-0.12110.6257-1.8284-1.6711.26070.65050.0671-0.16950.83580.01470.6812117.201114.8218177.1943
184.75310.9753-1.31796.8597-3.93845.64870.10310.5055-0.3691-0.253-0.14860.07060.0560.1942-0.00850.21590.02640.01490.3983-0.09260.3555114.19013.3728183.7239
195.68291.8762-2.87733.6983-5.91279.45870.1721-0.77580.4977-0.0142-0.55650.00070.1240.72290.29310.72210.12540.32880.6968-0.00911.111113.8902-9.4316194.3572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 112 )
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 141 )
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 212 )
4X-RAY DIFFRACTION4chain 'A' and (resid 213 through 354 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 6 )
6X-RAY DIFFRACTION6chain 'B' and (resid 7 through 16 )
7X-RAY DIFFRACTION7chain 'B' and (resid 17 through 22 )
8X-RAY DIFFRACTION8chain 'B' and (resid 23 through 49 )
9X-RAY DIFFRACTION9chain 'B' and (resid 50 through 59 )
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 70 )
11X-RAY DIFFRACTION11chain 'B' and (resid 77 through 82 )
12X-RAY DIFFRACTION12chain 'B' and (resid 83 through 96 )
13X-RAY DIFFRACTION13chain 'C' and (resid 48 through 262 )
14X-RAY DIFFRACTION14chain 'C' and (resid 263 through 353 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 44 )
16X-RAY DIFFRACTION16chain 'D' and (resid 45 through 71 )
17X-RAY DIFFRACTION17chain 'D' and (resid 72 through 82 )
18X-RAY DIFFRACTION18chain 'D' and (resid 83 through 94 )
19X-RAY DIFFRACTION19chain 'D' and (resid 95 through 99 )

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