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- PDB-2cbl: N-TERMINAL DOMAIN OF CBL IN COMPLEX WITH ITS BINDING SITE ON ZAP-70 -

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Basic information

Entry
Database: PDB / ID: 2cbl
TitleN-TERMINAL DOMAIN OF CBL IN COMPLEX WITH ITS BINDING SITE ON ZAP-70
Components
  • PROTO-ONCOGENE CBL
  • ZAP-70
KeywordsCOMPLEX (PROTO-ONCOGENE/PEPTIDE) / PROTO-ONCOGENE / SIGNAL TRANSDUCTION / PHOSPHOTYROSINE BINDING / SH2 / COMPLEX (PROTO-ONCOGENE-PEPTIDE) / COMPLEX (PROTO-ONCOGENE-PEPTIDE) 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 / 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: 2.1 Å
AuthorsMeng, W. / Sawasdikosol, S. / Burakoff, S.J. / Eck, M.J.
CitationJournal: Nature / Year: 1999
Title: Structure of the amino-terminal domain of Cbl complexed to its binding site on ZAP-70 kinase.
Authors: Meng, W. / Sawasdikosol, S. / Burakoff, S.J. / Eck, M.J.
History
DepositionAug 28, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 3, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / 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: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.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
Revision 2.1Oct 30, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTO-ONCOGENE CBL
B: ZAP-70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8143
Polymers36,7742
Non-polymers401
Water6,143341
1
A: PROTO-ONCOGENE CBL
B: ZAP-70
hetero molecules

A: PROTO-ONCOGENE CBL
B: ZAP-70
hetero molecules

A: PROTO-ONCOGENE CBL
B: ZAP-70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4439
Polymers110,3236
Non-polymers1203
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Unit cell
Length a, b, c (Å)123.380, 123.380, 56.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

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Components

#1: Protein PROTO-ONCOGENE CBL


Mass: 35429.961 Da / Num. of mol.: 1 / Fragment: DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P22681
#2: Protein/peptide ZAP-70


Mass: 1344.275 Da / Num. of mol.: 1 / Fragment: BINDING SITE FRAGMENT
Source method: isolated from a genetically manipulated source
References: UniProt: P43403*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
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: 3.18 Å3/Da / Density % sol: 61 %
Crystal growpH: 6.1 / Details: pH 6.1
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG80001reservoir
20.2 Mcalcium acetate1reservoir
32 mMdithiothreitol1reservoir
40.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: MARRESEARCH / Detector: CCD / Date: May 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. obs: 20620 / % possible obs: 76.9 % / Redundancy: 1.74 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 1 % / Rmerge(I) obs: 0.023 / Mean I/σ(I) obs: 1.5 / % possible all: 42.3
Reflection
*PLUS
Num. measured all: 35952

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CBL-N

Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2.1
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1047 5 %EVERY 20TH REFLECTION
Rwork0.173 ---
obs0.173 20620 76.9 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 1 340 2916
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.84
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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