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- PDB-1yvh: Crystal Structure of the c-Cbl TKB Domain in Complex with the APS... -

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Basic information

Entry
Database: PDB / ID: 1yvh
TitleCrystal Structure of the c-Cbl TKB Domain in Complex with the APS pTyr-618 Phosphopeptide
Components
  • 13-mer fragment of SH2 and PH domain-containing adapter protein APS
  • CBL E3 ubiquitin protein ligase
KeywordsLIGASE / SIGNALING PROTEIN / IMMUNE SYSTEM / X-RAY CRYSTALLOGRAPHY / PHOSPHOTYROSINE / ADAPTER PROTEIN
Function / homology
Function and homology information


Regulation of KIT signaling / Factors involved in megakaryocyte development and platelet production / antigen receptor-mediated signaling pathway / regulation of platelet-derived growth factor receptor-alpha signaling pathway / regulation of Ras protein signal transduction / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / B-1 B cell homeostasis / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding ...Regulation of KIT signaling / Factors involved in megakaryocyte development and platelet production / antigen receptor-mediated signaling pathway / regulation of platelet-derived growth factor receptor-alpha signaling pathway / regulation of Ras protein signal transduction / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / B-1 B cell homeostasis / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / transmembrane receptor protein tyrosine kinase adaptor activity / regulation of metabolic process / positive regulation of epidermal growth factor receptor signaling pathway / Interleukin-6 signaling / Regulation of KIT signaling / mast cell degranulation / response to starvation / negative regulation of epidermal growth factor receptor signaling pathway / response to testosterone / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / regulation of immune response / brown fat cell differentiation / protein autoubiquitination / stress fiber / ruffle / cellular response to platelet-derived growth factor stimulus / signaling adaptor activity / ephrin receptor binding / phosphotyrosine residue binding / FLT3 signaling by CBL mutants / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / SH2 domain binding / InlB-mediated entry of Listeria monocytogenes into host cell / response to activity / response to gamma radiation / actin filament / B cell receptor signaling pathway / Regulation of signaling by CBL / 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 / Spry regulation of FGF signaling / Constitutive Signaling by EGFRvIII / cytokine-mediated signaling pathway / Negative regulation of MET activity / 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 / insulin receptor signaling pathway / nervous system development / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / actin cytoskeleton organization / growth cone / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / protein ubiquitination / cilium / 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 / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SH2B2, SH2 domain / Phenylalanine zipper / Phenylalanine zipper superfamily / Phenylalanine zipper / SH2B adapter protein / 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 ...SH2B2, SH2 domain / Phenylalanine zipper / Phenylalanine zipper superfamily / Phenylalanine zipper / SH2B adapter protein / 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 / 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 / PH domain / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / PH domain profile. / Pleckstrin homology domain. / Ring finger / Pleckstrin homology domain / 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 / PH-like domain superfamily / 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 / SH2B adapter protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHu, J. / Hubbard, S.R.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural Characterization of a Novel Cbl Phosphotyrosine Recognition Motif in the APS Family of Adapter Proteins
Authors: Hu, J. / Hubbard, S.R.
History
DepositionFeb 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CBL E3 ubiquitin protein ligase
B: 13-mer fragment of SH2 and PH domain-containing adapter protein APS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8593
Polymers39,8352
Non-polymers241
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-4 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.257, 122.257, 55.131
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Cell settinghexagonal
Space group name H-MP6

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Components

#1: Protein CBL E3 ubiquitin protein ligase / E.C.6.3.2.- / Signal transduction protein CBL / Proto-oncogene c-CBL / Casitas B-lineage lymphoma proto- oncogene ...Signal transduction protein CBL / Proto-oncogene c-CBL / Casitas B-lineage lymphoma proto- oncogene / RING finger protein 55


Mass: 38192.090 Da / Num. of mol.: 1 / Fragment: Tyrosine kinase binding domain, residues 25-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide 13-mer fragment of SH2 and PH domain-containing adapter protein APS / APS adapter protein


Mass: 1642.665 Da / Num. of mol.: 1 / Fragment: pTyr-618 phosphopeptide / Source method: obtained synthetically / Details: sequence appears in Rattus norvegicus, gene APS / References: UniProt: Q9Z200
#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.: 188 / 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: 3.1 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: PEG 8000, magnesium acetate, sodium cacodylate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979
DetectorDetector: CCD / Date: Feb 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 29857 / Num. obs: 29857 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.061

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CBL

2cbl


Resolution: 2.05→30 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1424 4.8 %RANDOM
Rwork0.209 ---
all0.2091 29732 --
obs0.2091 29028 97.6 %-
Solvent computationBsol: 54.8 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.543 Å20.836 Å20 Å2
2--3.543 Å20 Å2
3----7.087 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 0 1 188 2754
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.168
X-RAY DIFFRACTIONc_dihedral_angle_d0.759
X-RAY DIFFRACTIONc_improper_angle_d0.759
X-RAY DIFFRACTIONc_mcbond_it0.8221.5
X-RAY DIFFRACTIONc_scbond_it1.2342
X-RAY DIFFRACTIONc_mcangle_it1.4252
X-RAY DIFFRACTIONc_scangle_it1.9272.5

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