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- PDB-4a4b: Structure of modified phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex -

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Basic information

Entry
Database: PDB / ID: 4a4b
TitleStructure of modified phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex
Components
  • E3 UBIQUITIN-PROTEIN LIGASE CBL
  • TYROSINE-PROTEIN KINASE ZAP-70
  • UBIQUITIN-CONJUGATING ENZYME E2 D2
KeywordsLIGASE/TRANSFERASE / LIGASE-TRANSFERASE COMPLEX
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 / (E3-independent) E2 ubiquitin-conjugating enzyme / beta 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 / (E3-independent) E2 ubiquitin-conjugating enzyme / beta selection / positive thymic T cell selection / positive regulation of alpha-beta T cell differentiation / positive regulation of T cell differentiation / Regulation of KIT signaling / positive regulation of epidermal growth factor receptor signaling pathway / T cell receptor complex / E2 ubiquitin-conjugating enzyme / mast cell degranulation / Interleukin-6 signaling / response to starvation / response to testosterone / Translocation of ZAP-70 to Immunological synapse / negative regulation of epidermal growth factor receptor signaling pathway / B cell activation / TGF-beta receptor signaling activates SMADs / ubiquitin conjugating enzyme activity / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / protein monoubiquitination / protein K48-linked ubiquitination / 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 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / response to activity / PINK1-PRKN Mediated Mitophagy / response to gamma radiation / Negative regulators of DDX58/IFIH1 signaling / non-membrane spanning protein tyrosine kinase activity / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / Peroxisomal protein import / non-specific protein-tyrosine kinase / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Regulation of TNFR1 signaling / Negative regulation of FGFR1 signaling / EGFR downregulation / peptidyl-tyrosine phosphorylation / calcium-mediated signaling / cellular response to nerve growth factor stimulus / Spry regulation of FGF signaling / Constitutive Signaling by EGFRvIII / Negative regulation of MET activity / protein modification process / cytokine-mediated signaling pathway / Inactivation of CSF3 (G-CSF) signaling / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / positive regulation of receptor-mediated endocytosis / SH3 domain binding / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / male gonad development / protein polyubiquitination / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / cell-cell junction / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / Neddylation / growth cone / ubiquitin-dependent protein catabolic process / protein tyrosine kinase activity / response to ethanol / cellular response to hypoxia / adaptive immune response / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / intracellular signal transduction
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 Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / : / 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. / Zinc finger RING-type profile. / Src homology 2 domains / SH2 domain / 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 / Roll / 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 / Ubiquitin-conjugating enzyme E2 D2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.789 Å
AuthorsDou, H. / Buetow, L. / Hock, A. / Sibbet, G.J. / Vousden, K.H. / Huang, D.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural Basis for Autoinhibition and Phosphorylation-Dependent Activation of C-Cbl
Authors: Dou, H. / Buetow, L. / Hock, A. / Sibbet, G.J. / Vousden, K.H. / Huang, D.T.
History
DepositionOct 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE CBL
B: TYROSINE-PROTEIN KINASE ZAP-70
C: UBIQUITIN-CONJUGATING ENZYME E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4076
Polymers63,2363
Non-polymers1713
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-14.3 kcal/mol
Surface area31200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.112, 74.112, 449.706
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE CBL / CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE / PROTO-ONCOGENE C-CBL / RING FINGER PROTEIN 55 / SIGNAL ...CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE / PROTO-ONCOGENE C-CBL / RING FINGER PROTEIN 55 / SIGNAL TRANSDUCTION PROTEIN CBL / C-CBL


Mass: 45136.805 Da / Num. of mol.: 1
Fragment: TKB DOMAIN, LINKER HELIX REGION, AND RING DOMAIN, RESIDUES 47-435
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Protein UBIQUITIN-CONJUGATING ENZYME E2 D2 / UBIQUITIN CARRIER PROTEIN D2 / UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2 / UBIQUITIN-CONJUGATING ...UBIQUITIN CARRIER PROTEIN D2 / UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2 / UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2 / UBIQUITIN-PROTEIN LIGASE D2 / UBCH5B


Mass: 16755.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: P62837, ubiquitin-protein ligase

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Protein/peptide , 1 types, 1 molecules B

#2: Protein/peptide TYROSINE-PROTEIN KINASE ZAP-70 / 70 KDA ZETA-ASSOCIATED PROTEIN / SYK-RELATED TYROSINE KINASE / ZAP-70


Mass: 1344.275 Da / Num. of mol.: 1 / Fragment: ZAP-70 PEPTIDE, RESIDUES 286-297 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
References: UniProt: P43403, non-specific protein-tyrosine kinase

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Non-polymers , 3 types, 20 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 368 TO PHE
Has protein modificationY
Nonpolymer detailsCALCIUM (CA): REQUIRED FOR STABILITY OF CHAIN A ZINC (ZN): REQUIRED FOR STABILITY OF CHAIN A
Sequence detailsN-TERMINAL GS RESULTED FROM CLONING AND TEV CLEAVAGE. Y371 IS PHOSPHORYLATED. Y368 IS MUTATED TO ...N-TERMINAL GS RESULTED FROM CLONING AND TEV CLEAVAGE. Y371 IS PHOSPHORYLATED. Y368 IS MUTATED TO PHE. CORRESPONDS TO 286-297 IN HUMAN ZAP-70 SEQUENCE. Y7 IS PHOSPHORYLATED.

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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: 2.9 Å3/Da / Density % sol: 57.9 % / Description: NONE
Crystal growpH: 7.5
Details: 31-35% PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), 0.2 M KCL, 50 MM HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2011 / Details: SLITS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.79→30 Å / Num. obs: 19621 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 19 % / Biso Wilson estimate: 80.48 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.9
Reflection shellResolution: 2.79→2.94 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.3 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2CBL, 2ESK, 1FBV.

2cbl

2esk

1fbv


Resolution: 2.789→28.725 Å / SU ML: 0.71 / σ(F): 1.36 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 992 5.1 %
Rwork0.1874 --
obs0.1913 19374 99.36 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.918 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso mean: 84.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.3108 Å20 Å20 Å2
2--1.3108 Å20 Å2
3----2.6216 Å2
Refinement stepCycle: LAST / Resolution: 2.789→28.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 3 17 4284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094383
X-RAY DIFFRACTIONf_angle_d1.2275965
X-RAY DIFFRACTIONf_dihedral_angle_d15.6431589
X-RAY DIFFRACTIONf_chiral_restr0.088648
X-RAY DIFFRACTIONf_plane_restr0.007770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.789-2.93590.36071460.29942452X-RAY DIFFRACTION97
2.9359-3.11970.30851400.24122563X-RAY DIFFRACTION100
3.1197-3.36020.32311480.21852564X-RAY DIFFRACTION100
3.3602-3.69770.32361420.20692599X-RAY DIFFRACTION100
3.6977-4.23130.24781390.18612610X-RAY DIFFRACTION100
4.2313-5.32550.23981360.15522717X-RAY DIFFRACTION100
5.3255-28.72680.23631410.17492877X-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)
11.30820.5145-0.13893.4041-1.57652.26810.4040.13490.46850.1030.17010.5688-0.7304-0.7925-0.34210.62360.19670.13960.4381-0.05030.60189.537916.150524.9797
23.2432-0.45160.80483.76061.01752.50350.2014-0.82010.24280.5592-0.02620.043-0.5439-0.0596-0.02550.6789-0.02990.17250.2449-0.18540.258321.949113.821231.7395
32.09471.16010.08273.58460.16484.30850.17370.2079-0.2878-0.1388-0.0587-0.6158-0.06921.257-0.20960.3982-0.0104-0.06570.2109-0.29830.132839.614612.12723.8625
41.9660.8614-0.60576.11960.05152.18110.22440.0654-0.52370.5416-0.1112-0.54670.76040.9161-0.15821.03560.3115-0.2210.3388-0.25670.695433.6362-15.985220.0001
53.1801-0.2852-1.59936.405-3.54062.93440.36860.1809-0.356-1.01260.5110.26440.38630.3708-0.34690.66220.0077-0.00360.5377-0.27840.464635.29648.83619.6774
63.67492.16761.29762.19972.53186.21020.0072-0.1972-0.67410.79980.3978-0.16292.13010.5416-0.43481.41940.193-0.03460.4725-0.06510.611424.9135-29.57765.1769
73.86443.7764-2.03965.1491-3.35962.35530.61480.63280.21230.39190.47640.33320.790.0265-0.31870.97110.04880.03010.4806-0.16410.528521.5539-28.1131-2.6893
83.83982.86382.11654.2043-0.96374.29451.0272-1.0608-0.19530.93640.27920.77940.8859-1.2787-0.96041.3173-0.56140.27320.85220.11010.99850.6726-28.84811.7577
93.1983-0.05251.00323.72060.44654.2581-0.10390.8956-0.54160.01020.70220.10490.46150.1282-0.48710.6859-0.08370.15940.3866-0.08860.632615.7255-19.9445-4.0157
103.70821.63410.4473.83080.65744.94190.1787-0.09550.36940.556-0.22190.51720.6847-0.71170.12950.9616-0.25160.34660.2223-0.06570.743615.0289-18.04475.8196
113.70261.62033.06921.02031.09962.73540.0108-0.59481.4839-0.166-0.19041.65370.2194-1.0421-0.07170.8588-0.16470.10040.7519-0.28561.746-2.2395-19.2695-4.831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 48:112)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 113:212)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 213:353)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 354:435)
5X-RAY DIFFRACTION5CHAIN B
6X-RAY DIFFRACTION6CHAIN C AND (RESSEQ 2:28)
7X-RAY DIFFRACTION7CHAIN C AND (RESSEQ 29:38)
8X-RAY DIFFRACTION8CHAIN C AND (RESSEQ 39:48)
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 49:84)
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 85:111)
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 112:147)

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