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- PDB-5o76: Structure of phosphoY371 c-CBL in complex with ZAP70-peptide and ... -

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Basic information

Entry
Database: PDB / ID: 5o76
TitleStructure of phosphoY371 c-CBL in complex with ZAP70-peptide and UbV.pCBL ubiquitin variant
Components
  • E3 ubiquitin-protein ligase CBL
  • Tyrosine protein kinase ZAP70 peptide
  • UbV.pCBL ubiquitin variant
KeywordsLIGASE / E3 ring ligase / ubiquitin variant
Function / homology
Function and homology information


T cell aggregation / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / beta selection / positive thymic T cell selection ...T cell aggregation / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / beta selection / positive thymic T cell selection / positive regulation of alpha-beta T cell differentiation / positive regulation of T cell differentiation / positive regulation of epidermal growth factor receptor signaling pathway / Interleukin-6 signaling / Regulation of KIT signaling / T cell receptor complex / mast cell degranulation / response to starvation / Translocation of ZAP-70 to Immunological synapse / negative regulation of epidermal growth factor receptor signaling pathway / response to testosterone / B cell activation / TGF-beta receptor signaling activates SMADs / RHOH GTPase cycle / Generation of second messenger molecules / T cell differentiation / immunological synapse / protein monoubiquitination / T cell migration / protein autoubiquitination / Nuclear events stimulated by ALK signaling in cancer / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / phosphotyrosine residue binding / FLT3 signaling by CBL mutants / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / positive regulation of calcium-mediated signaling / T cell activation / InlB-mediated entry of Listeria monocytogenes into host cell / response to activity / response to gamma radiation / non-membrane spanning protein tyrosine kinase activity / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / EGFR downregulation / cellular response to nerve growth factor stimulus / calcium-mediated signaling / Spry regulation of FGF signaling / Constitutive Signaling by EGFRvIII / cytokine-mediated signaling pathway / Negative regulation of MET activity / peptidyl-tyrosine phosphorylation / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / SH3 domain binding / positive regulation of receptor-mediated endocytosis / male gonad development / protein polyubiquitination / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / cell-cell junction / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / T cell receptor signaling pathway / Clathrin-mediated endocytosis / growth cone / ubiquitin-dependent protein catabolic process / protein tyrosine kinase activity / cellular response to hypoxia / adaptive immune response / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / protein ubiquitination / immune response / cilium / protein phosphorylation / cadherin binding / membrane raft / symbiont entry into host cell / focal adhesion / calcium ion binding / DNA damage response / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / zinc ion binding / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Adaptor protein Cbl, N-terminal domain / 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 / 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. / Prokaryotic RING finger family 4 / Adaptor protein Cbl, N-terminal domain superfamily / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / Transcription Elongation Factor S-II; Chain A / 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) / SH2 domain / SHC Adaptor Protein / UBA-like superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / : / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Zinc finger, RING/FYVE/PHD-type / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CBL / Tyrosine-protein kinase ZAP-70
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.473 Å
AuthorsGabrielsen, M. / Buetow, L. / Huang, D.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC596/A23278 United Kingdom
European Research Council647849 United Kingdom
CitationJournal: Mol. Cell / Year: 2017
Title: A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants.
Authors: Gabrielsen, M. / Buetow, L. / Nakasone, M.A. / Ahmed, S.F. / Sibbet, G.J. / Smith, B.O. / Zhang, W. / Sidhu, S.S. / Huang, D.T.
History
DepositionJun 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Tyrosine protein kinase ZAP70 peptide
C: E3 ubiquitin-protein ligase CBL
D: Tyrosine protein kinase ZAP70 peptide
E: UbV.pCBL ubiquitin variant
F: UbV.pCBL ubiquitin variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,58112
Polymers111,2396
Non-polymers3426
Water4,234235
1
A: E3 ubiquitin-protein ligase CBL
B: Tyrosine protein kinase ZAP70 peptide
E: UbV.pCBL ubiquitin variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7906
Polymers55,6203
Non-polymers1713
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: E3 ubiquitin-protein ligase CBL
D: Tyrosine protein kinase ZAP70 peptide
F: UbV.pCBL ubiquitin variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7906
Polymers55,6203
Non-polymers1713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.790, 101.281, 117.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACEF

#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: 45136.805 Da / Num. of mol.: 2 / Mutation: Y368F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 / Plasmid: pGEX4T.1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P22681, RING-type E3 ubiquitin transferase
#3: Protein UbV.pCBL ubiquitin variant


Mass: 9138.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Protein/peptide , 1 types, 2 molecules BD

#2: Protein/peptide Tyrosine protein kinase ZAP70 peptide


Mass: 1344.275 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P43403*PLUS

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Non-polymers , 3 types, 241 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.22 Å3/Da / Density meas: 44.72 Mg/m3 / Density % sol: 51.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M monosaccharides, 0.1 M Buffer 1 pH 6.5, 50% Precipitant 2, Morpheus screen

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97632 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97632 Å / Relative weight: 1
ReflectionResolution: 2.473→101.281 Å / Num. obs: 38315 / % possible obs: 93.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 59.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.066 / Net I/σ(I): 13.9
Reflection shellResolution: 2.473→2.515 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.155 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2007 / CC1/2: 0.796 / Rpim(I) all: 0.667 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A4B

4a4b


Resolution: 2.473→35.34 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.884 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 4.595 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.627 / SU Rfree Blow DPI: 0.283 / SU Rfree Cruickshank DPI: 0.285
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1870 4.9 %RANDOM
Rwork0.218 ---
obs0.22 38141 92.6 %-
Displacement parametersBiso mean: 69.77 Å2
Baniso -1Baniso -2Baniso -3
1-20.8314 Å20 Å20 Å2
2---16.6367 Å20 Å2
3----4.1947 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: 1 / Resolution: 2.473→35.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7384 0 70 235 7689
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089457HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9513831HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3207SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes194HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1187HARMONIC5
X-RAY DIFFRACTIONt_it9457HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.1
X-RAY DIFFRACTIONt_other_torsion17.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1000SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10254SEMIHARMONIC4
LS refinement shellResolution: 2.47→2.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.276 144 4.81 %
Rwork0.241 2849 -
all0.243 2993 -
obs--95.7 %
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)
12.8525-0.14090.85580.8504-0.37030.4449-0.00650.1426-0.115-0.0180.04010.00110.05790.0302-0.0336-0.05510.01290.02-0.1295-0.0107-0.1199-7.50417.15-0.405
22.7814-0.9146-1.00430.20850.30611.12550.1267-0.0089-0.0734-0.0698-0.0262-0.0505-0.0176-0.1332-0.1005-0.09-0.0004-0.0408-0.0781-0.0809-0.11912.0726-25.0854-8.0126
30.3941-0.1924-0.63810.02580.5780.3546-0.00040.01390.0016-0.0099-0.0057-0.00770.0075-0.0070.0061-0.0074-0.00510.04020.0336-0.0208-0.037423.088-15.4585-18.0299
43.55492.18320.60375.57970.56235.4646-0.0702-0.2709-0.38320.4650.13720.08360.2861-0.0953-0.067-0.10450.03120.0619-0.20670.1093-0.000817.9964-0.22719.3751
53.9233-0.3518-0.47232.66591.05813.75190.00480.3593-0.1778-0.2160.00810.06340.25820.3515-0.01290.05070.169-0.14340.0023-0.0944-0.21538.4621-43.1319-27.1982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ C|* }
3X-RAY DIFFRACTION3{ D|* }
4X-RAY DIFFRACTION4{ E|* }
5X-RAY DIFFRACTION5{ F|* }

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