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- PDB-2y1n: Structure of c-Cbl-ZAP-70 peptide complex -

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Basic information

Entry
Database: PDB / ID: 2y1n
TitleStructure of c-Cbl-ZAP-70 peptide complex
Components
  • E3 UBIQUITIN-PROTEIN LIGASE
  • TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE
KeywordsLIGASE/TRANSFERASE / LIGASE-TRANSFERASE COMPLEX / UBIQUITIN RING E3 LIGASE
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 / T cell receptor complex / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling / response to starvation / negative regulation of epidermal growth factor receptor signaling pathway / Translocation of ZAP-70 to Immunological synapse / extrinsic component of cytoplasmic side of plasma membrane / cellular response to platelet-derived growth factor stimulus / TGF-beta receptor signaling activates SMADs / response to testosterone / protein monoubiquitination / B cell activation / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / T cell migration / protein autoubiquitination / Nuclear events stimulated by ALK signaling in cancer / cell surface receptor protein tyrosine kinase signaling pathway / FLT3 signaling by CBL mutants / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / phosphotyrosine residue binding / ephrin receptor binding / positive regulation of calcium-mediated signaling / T cell activation / cellular response to nerve growth factor stimulus / InlB-mediated entry of Listeria monocytogenes into host cell / response to gamma radiation / response to activity / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / EGFR downregulation / non-membrane spanning protein tyrosine kinase activity / Negative regulation of FGFR4 signaling / calcium-mediated signaling / Negative regulation of FGFR1 signaling / Constitutive Signaling by EGFRvIII / Spry regulation of FGF signaling / RING-type E3 ubiquitin transferase / Negative regulation of MET activity / cilium / receptor tyrosine kinase binding / cytokine-mediated signaling pathway / SH3 domain binding / peptidyl-tyrosine phosphorylation / positive regulation of receptor-mediated endocytosis / protein polyubiquitination / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin-protein transferase activity / male gonad development / ubiquitin protein ligase activity / cell-cell junction / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / T cell receptor signaling pathway / cellular response to hypoxia / growth cone / ubiquitin-dependent protein catabolic process / protein tyrosine kinase activity / response to ethanol / adaptive immune response / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / protein ubiquitination / cadherin binding / immune response / symbiont entry into host cell / protein phosphorylation / membrane raft / innate immune response / signaling receptor binding / focal adhesion / DNA damage response / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / ATP binding / plasma membrane
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 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / SH2 domain / SHC Adaptor Protein / UBA-like superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / : / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Ring finger / SH2 domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / 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: 1.999 Å
AuthorsDou, H. / Sibbet, G.J. / 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
DepositionDec 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Feb 15, 2012Group: Other
Revision 1.3Dec 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_conn_type / 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_asym_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_asym_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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE
B: TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE
C: E3 UBIQUITIN-PROTEIN LIGASE
D: TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,88810
Polymers92,5464
Non-polymers3426
Water6,125340
1
C: E3 UBIQUITIN-PROTEIN LIGASE
D: TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4445
Polymers46,2732
Non-polymers1713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-21.3 kcal/mol
Surface area18450 Å2
MethodPISA
2
A: E3 UBIQUITIN-PROTEIN LIGASE
B: TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4445
Polymers46,2732
Non-polymers1713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-21.4 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.570, 93.570, 189.599
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 44928.695 Da / Num. of mol.: 2 / Fragment: RESIDUES 47-435
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)
References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE


Mass: 1344.275 Da / Num. of mol.: 2 / Fragment: PEPTIDE, RESIDUES 286-297 / Source method: obtained synthetically
Details: ZAP-70 PEPTIDE (TLNSDG(P)YTPEPA) WITH PHOSPHOTYROSINE AT POSITION 7
Source: (synth.) HOMO SAPIENS (human)
References: UniProt: P43403, non-specific protein-tyrosine kinase
#3: Chemical
ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.83 % / Description: NONE
Crystal growDetails: 18-20% (W/V) PEG 3350, 0.2 M AMMONIUM FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 8, 2010
RadiationMonochromator: SYNCHROTRON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.395
ReflectionResolution: 2→50 Å / Num. obs: 63238 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 30.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CBL

2cbl


Resolution: 1.999→45.423 Å / σ(F): 1.36 / Phase error: 30.1 / Stereochemistry target values: TWIN_LSQ_F
Details: RESIDUES OMITTED DUE TO POORLY DEFINED ELECTRON DENSITY. CHAIN A RESIDUES 355-361, CHAIN C RESIDUES 355-35 CHAINS B AND D RESIDUES 1-3. DUE TO POORLY DEFINED ELECTRON DENSITY, LYS53 AND ...Details: RESIDUES OMITTED DUE TO POORLY DEFINED ELECTRON DENSITY. CHAIN A RESIDUES 355-361, CHAIN C RESIDUES 355-35 CHAINS B AND D RESIDUES 1-3. DUE TO POORLY DEFINED ELECTRON DENSITY, LYS53 AND LYS54 IN CHAINS A AND C WERE BUILT AS ALANINES.
RfactorNum. reflection% reflection
Rfree0.1804 3219 5.1 %
Rwork0.1582 --
obs0.159 63238 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.127 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 39.82 Å2
Baniso -1Baniso -2Baniso -3
1-5.0461 Å20 Å20 Å2
2--5.0461 Å20 Å2
3----10.0922 Å2
Refinement stepCycle: LAST / Resolution: 1.999→45.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6277 0 6 340 6623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086434
X-RAY DIFFRACTIONf_angle_d1.1428695
X-RAY DIFFRACTIONf_dihedral_angle_d16.142406
X-RAY DIFFRACTIONf_chiral_restr0.069928
X-RAY DIFFRACTIONf_plane_restr0.0061114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9993-2.03380.27041620.26182978X-RAY DIFFRACTION94
2.0338-2.07070.26231700.25012961X-RAY DIFFRACTION94
2.0707-2.11060.2241620.23782997X-RAY DIFFRACTION95
2.1106-2.15360.24421500.21412984X-RAY DIFFRACTION95
2.1536-2.20040.23561570.20853002X-RAY DIFFRACTION95
2.2004-2.25160.23811650.21352997X-RAY DIFFRACTION95
2.2516-2.30790.22111770.21622970X-RAY DIFFRACTION94
2.3079-2.37030.2151530.20363010X-RAY DIFFRACTION95
2.3703-2.440.21541710.19452993X-RAY DIFFRACTION95
2.44-2.51870.22261480.19393031X-RAY DIFFRACTION95
2.5187-2.60870.20011660.19242986X-RAY DIFFRACTION95
2.6087-2.7130.21411600.18853001X-RAY DIFFRACTION95
2.713-2.83640.21921650.18263008X-RAY DIFFRACTION95
2.8364-2.98580.1961550.17542979X-RAY DIFFRACTION95
2.9858-3.17270.17921670.17063001X-RAY DIFFRACTION95
3.1727-3.41730.15921420.14613023X-RAY DIFFRACTION96
3.4173-3.76060.15191480.12913041X-RAY DIFFRACTION95
3.7606-4.30330.15691610.11163006X-RAY DIFFRACTION95
4.3033-5.41620.1341760.11122998X-RAY DIFFRACTION94
5.4162-29.44370.15031640.12843027X-RAY DIFFRACTION95

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