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- PDB-1b47: STRUCTURE OF THE N-TERMINAL DOMAIN OF CBL IN COMPLEX WITH ITS BIN... -

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Basic information

Entry
Database: PDB / ID: 1b47
TitleSTRUCTURE OF THE N-TERMINAL DOMAIN OF CBL IN COMPLEX WITH ITS BINDING SITE IN ZAP-70
ComponentsCBL
KeywordsSIGNAL TRANSDUCTION / CBL / SH2 / PROTO-ONCOGENE
Function / homology
Function and homology information


regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / entry of bacterium into host cell / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / entry of bacterium into host cell / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling / response to testosterone / cellular response to platelet-derived growth factor stimulus / negative regulation of epidermal growth factor receptor signaling pathway / response to starvation / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / protein autoubiquitination / FLT3 signaling by CBL mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / phosphotyrosine residue binding / ephrin receptor binding / InlB-mediated entry of Listeria monocytogenes into host cell / cellular response to nerve growth factor stimulus / response to activity / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / response to gamma radiation / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / EGFR downregulation / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / Constitutive Signaling by EGFRvIII / RING-type E3 ubiquitin transferase / Negative regulation of MET activity / cilium / receptor tyrosine kinase binding / cytokine-mediated signaling pathway / SH3 domain binding / positive regulation of receptor-mediated endocytosis / protein polyubiquitination / ubiquitin-protein transferase activity / Signaling by CSF1 (M-CSF) in myeloid cells / male gonad development / ubiquitin protein ligase activity / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / growth cone / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cadherin binding / membrane raft / focal adhesion / DNA damage response / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / plasma membrane / cytosol
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 / 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 / UBA-like superfamily / SHC Adaptor Protein / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CBL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 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
DepositionJan 6, 1999Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.process_site / _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.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.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CBL
B: CBL
C: CBL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2396
Polymers106,1193
Non-polymers1203
Water11,998666
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.960, 105.480, 84.920
Angle α, β, γ (deg.)90.00, 92.06, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.399672, 0.916202, -0.028918), (-0.914736, -0.396594, 0.077273), (0.059329, 0.057336, 0.996591)29.8495, 35.2372, -30.3331
2given(-0.746434, -0.66218, 0.065977), (0.664788, -0.737557, 0.118599), (-0.029872, 0.132387, 0.990748)51.2264, -11.0673, -56.081

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Components

#1: Protein CBL / PROTO-ONCOGENE C-CBL


Mass: 35372.910 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PGEX 4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P22681
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 20

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60 %
Crystal growpH: 5.6 / Details: pH 5.6
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: ADSC / Detector: CCD / Date: Dec 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 70918 / % possible obs: 99.3 % / Redundancy: 2.5 % / Biso Wilson estimate: 45.12 Å2 / Rsym value: 0.067 / Net I/σ(I): 3.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.391 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 178845 / Rmerge(I) obs: 0.067

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Processing

Software
NameVersionClassification
HEAVYmodel building
PATSOLmodel building
CNS0.4refinement
MOSFLMdata reduction
CCP4data scaling
HEAVYphasing
PATSOLphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→50 Å / Data cutoff high rms absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3595 5 %RANDOM
Rwork0.218 ---
obs0.218 70918 99.3 %-
Displacement parametersBiso mean: 47.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.489 Å20 Å20.066 Å2
2---4.825 Å20 Å2
3---8.314 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8092 0 3 666 8761
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.61
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.53
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d4.22
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1871.5
X-RAY DIFFRACTIONc_mcangle_it1.9132
X-RAY DIFFRACTIONc_scbond_it1.9272
X-RAY DIFFRACTIONc_scangle_it2.8452.5
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.36 374 5 %
Rwork0.28 6707 -
obs--99 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PA
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARA
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.53
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg4.22

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