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- PDB-1fbv: STRUCTURE OF A CBL-UBCH7 COMPLEX: RING DOMAIN FUNCTION IN UBIQUIT... -

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Basic information

Entry
Database: PDB / ID: 1fbv
TitleSTRUCTURE OF A CBL-UBCH7 COMPLEX: RING DOMAIN FUNCTION IN UBIQUITIN-PROTEIN LIGASES
Components
  • SIGNAL TRANSDUCTION PROTEIN CBL
  • UBIQUITIN-CONJUGATING ENZYME E12-18 KDA UBCH7
  • ZAP-70 PEPTIDE
KeywordsLIGASE / cbl / ubch7 / ZAP-70 / E2 / ubiquitin / E3 / phosphorylation / tyrosine kinase / ubiquitination / protein degradation
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 / cell cycle phase transition / ubiquitin-protein transferase activator activity / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding ...T cell aggregation / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / cell cycle phase transition / ubiquitin-protein transferase activator activity / 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 / protein K11-linked ubiquitination / positive regulation of alpha-beta T cell differentiation / positive regulation of protein targeting to mitochondrion / positive regulation of T cell differentiation / Regulation of KIT signaling / positive regulation of epidermal growth factor receptor signaling pathway / cellular response to glucocorticoid stimulus / T cell receptor complex / E2 ubiquitin-conjugating enzyme / mast cell degranulation / Interleukin-6 signaling / cellular response to steroid hormone stimulus / 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 / ubiquitin ligase complex / 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 / InlB-mediated entry of Listeria monocytogenes into host cell / positive regulation of protein ubiquitination / response to activity / PINK1-PRKN Mediated Mitophagy / response to gamma radiation / non-membrane spanning protein tyrosine kinase activity / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / 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 / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / positive regulation of receptor-mediated endocytosis / SH3 domain binding / Regulation of necroptotic cell death / 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 / 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 / growth cone / ubiquitin-dependent protein catabolic process / protein tyrosine kinase activity / response to ethanol / cellular response to hypoxia / adaptive immune response / transcription coactivator activity / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / intracellular signal transduction / protein phosphorylation
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 L3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsZheng, N. / Wang, P. / Jeffrey, P.D. / Pavletich, N.P.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structure of a c-Cbl-UbcH7 complex: RING domain function in ubiquitin-protein ligases.
Authors: Zheng, N. / Wang, P. / Jeffrey, P.D. / Pavletich, N.P.
History
DepositionJul 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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.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: SIGNAL TRANSDUCTION PROTEIN CBL
B: ZAP-70 PEPTIDE
C: UBIQUITIN-CONJUGATING ENZYME E12-18 KDA UBCH7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,33010
Polymers63,7193
Non-polymers6117
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-81 kcal/mol
Surface area26060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219, 219, 219
Angle α, β, γ (deg.)90, 90, 90
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein SIGNAL TRANSDUCTION PROTEIN CBL


Mass: 44813.609 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) / References: UniProt: P22681
#2: Protein/peptide ZAP-70 PEPTIDE


Mass: 1015.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED / References: UniProt: P43403*PLUS
#3: Protein UBIQUITIN-CONJUGATING ENZYME E12-18 KDA UBCH7


Mass: 17889.588 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) / References: UniProt: P68036, ubiquitin-protein ligase
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 8

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Sample preparation

CrystalDensity Matthews: 6.87 Å3/Da
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Sodium Citrate, Ammonium Sulfate,, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5
Details: c-Cbl:UbcH7:ZAP-70=1:1:3 at a molar ratio in a solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
127 mg/mlc-Cbl1drop
232 mg/mlUbcH71drop
340 mg/mlZAP-701drop
420 mM2-(N-Morpholino)ethanesulfonic acid1drop
5150 mM1dropNaCl
65 mMdithiothreitol1drop
7100 mMsodium citrate1reservoir
81.9-2.1 Mammonium sulfate1reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 38512 / % possible obs: 96.8 % / Num. measured all: 156681 / Rmerge(I) obs: 0.062

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 2.9→15 Å / σ(F): 2
RfactorNum. reflection
Rfree0.262 -
Rwork0.227 -
all-38512
obs-156681
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 27 0 4367
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 15 Å / Num. reflection obs: 34351 / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.92
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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