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- PDB-7siy: cCBL TKB domain in complex with pZAP70 peptide -

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Basic information

Entry
Database: PDB / ID: 7siy
TitlecCBL TKB domain in complex with pZAP70 peptide
Components
  • E3 ubiquitin-protein ligase CBL
  • Peptide from Tyrosine-protein kinase ZAP-70
KeywordsIMMUNE SYSTEM / cCBL / ZAP70 / phospho-Tyr
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. / 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 / : / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / 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 / Orthogonal Bundle / 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: 1.48 Å
AuthorsMurray, J.M. / Yu, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: cCBL TKB domain in complex with pZAP70 peptide
Authors: Murray, J.M. / Yu, C.
History
DepositionOct 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase CBL
Z: Peptide from Tyrosine-protein kinase ZAP-70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0673
Polymers36,0432
Non-polymers241
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.519, 123.519, 56.598
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Components on special symmetry positions
IDModelComponents
11Z-113-

HOH

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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: 35332.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 / Production host: Escherichia coli (E. coli)
References: UniProt: P22681, RING-type E3 ubiquitin transferase
#2: Protein/peptide Peptide from Tyrosine-protein kinase ZAP-70


Mass: 709.661 Da / Num. of mol.: 1 / Fragment: Residues 292-296 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P43403
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.46 Å3/Da / Density % sol: 64.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium formate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.476→61.759 Å / Num. obs: 78431 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 25.87 Å2 / CC1/2: 1 / Net I/σ(I): 7.9
Reflection shellResolution: 1.476→1.501 Å / Rmerge(I) obs: 8.11 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4096 / CC1/2: 0.346

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Processing

Software
NameVersionClassification
PHENIX1.19-4092_finalrefinement
autoPROCdata reduction
autoPROCdata scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OB2

3ob2


Resolution: 1.48→35.66 Å / SU ML: 0.2792 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 42.1915
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 3779 4.88 %RANDOM
Rwork0.2085 73605 --
obs0.2092 77384 93.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.84 Å2
Refinement stepCycle: LAST / Resolution: 1.48→35.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 5 372 2912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00442606
X-RAY DIFFRACTIONf_angle_d0.69143520
X-RAY DIFFRACTIONf_chiral_restr0.0695374
X-RAY DIFFRACTIONf_plane_restr0.0061446
X-RAY DIFFRACTIONf_dihedral_angle_d12.9583977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.490.77711500.8062482X-RAY DIFFRACTION85.59
1.49-1.510.66441430.73582711X-RAY DIFFRACTION95.32
1.51-1.530.587400.738724X-RAY DIFFRACTION24.78
1.53-1.560.63381410.63612833X-RAY DIFFRACTION98.28
1.56-1.580.57611450.55352938X-RAY DIFFRACTION99.36
1.58-1.60.50541490.50062867X-RAY DIFFRACTION99.8
1.6-1.630.49511170.46392906X-RAY DIFFRACTION99.67
1.63-1.660.38161650.43662915X-RAY DIFFRACTION99.9
1.66-1.690.33211500.41372861X-RAY DIFFRACTION99.37
1.69-1.720.38961460.38922904X-RAY DIFFRACTION99.48
1.72-1.760.48271370.35882872X-RAY DIFFRACTION99.44
1.76-1.80.3821650.33752897X-RAY DIFFRACTION99.35
1.8-1.840.31981420.31422898X-RAY DIFFRACTION99.84
1.84-1.880.31661620.29872904X-RAY DIFFRACTION99.64
1.88-1.930.32271210.28841971X-RAY DIFFRACTION68.59
1.93-1.990.2741330.28062904X-RAY DIFFRACTION99.64
1.99-2.050.2361540.21062894X-RAY DIFFRACTION99.25
2.05-2.130.2633920.2152241X-RAY DIFFRACTION75.65
2.13-2.210.20211180.18632910X-RAY DIFFRACTION99.44
2.21-2.310.22481100.19172358X-RAY DIFFRACTION80.79
2.31-2.440.21531530.18692931X-RAY DIFFRACTION99.68
2.44-2.590.19641730.1962895X-RAY DIFFRACTION99.77
2.59-2.790.23721520.18372936X-RAY DIFFRACTION99.87
2.79-3.070.19041570.17722921X-RAY DIFFRACTION99.94
3.07-3.510.16551680.16092932X-RAY DIFFRACTION99.94
3.51-4.420.15081630.14792951X-RAY DIFFRACTION99.97
4.43-35.660.18341330.15953049X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: 77.1643335649 Å / Origin y: 49.5434198896 Å / Origin z: 6.26342082223 Å
111213212223313233
T0.268435307636 Å2-0.0133868955451 Å20.0268307067043 Å2-0.28853433231 Å20.0642733814585 Å2--0.618455780707 Å2
L1.63674314549 °2-0.155463358313 °20.222466763934 °2-1.21604897297 °2-0.0252472828639 °2--0.82880637459 °2
S-0.0106772399437 Å °0.175021021441 Å °0.351092682857 Å °-0.171413081092 Å °-0.0470086430879 Å °-0.269630648827 Å °-0.079864545374 Å °0.0584347691142 Å °0.0677532040461 Å °
Refinement TLS groupSelection details: all

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