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- PDB-2oob: crystal structure of the UBA domain from Cbl-b ubiquitin ligase i... -

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Basic information

Entry
Database: PDB / ID: 2oob
Titlecrystal structure of the UBA domain from Cbl-b ubiquitin ligase in complex with ubiquitin
Components
  • E3 ubiquitin-protein ligase CBL-B
  • Ubiquitin
KeywordsLIGASE / protein-protein complex
Function / homology
Function and homology information


: / regulation of platelet-derived growth factor receptor-alpha signaling pathway / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B ...: / regulation of platelet-derived growth factor receptor-alpha signaling pathway / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Cyclin D associated events in G1 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / Interferon alpha/beta signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / RAS processing / Pexophagy / Inactivation of CSF3 (G-CSF) signaling / Negative regulation of FLT3 / Regulation of BACH1 activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Termination of translesion DNA synthesis / Ovarian tumor domain proteases / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of MAPK pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Iron uptake and transport / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / T cell anergy / positive regulation of T cell anergy / Activation of NF-kappaB in B cells / L13a-mediated translational silencing of Ceruloplasmin expression / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SRP-dependent cotranslational protein targeting to membrane / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling
Similarity search - Function
E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / 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. ...E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / 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 / Ubiquitin-associated (UBA) domain / Ubiquitin associated domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helicase, Ruva Protein; domain 3 / Ring finger / Ubiquitin conserved site / Ubiquitin domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain signature. / SH2 domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / EF-hand domain pair / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40 / E3 ubiquitin-protein ligase CBL-B
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKozlov, G. / Gehring, K.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural basis for ubiquitin-mediated dimerization and activation of the ubiquitin protein ligase Cbl-b.
Authors: Peschard, P. / Kozlov, G. / Lin, T. / Mirza, I.A. / Berghuis, A.M. / Lipkowitz, S. / Park, M. / Gehring, K.
History
DepositionJan 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase CBL-B
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)14,2332
Polymers14,2332
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.608, 54.784, 94.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-110-

HOH

21B-150-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase CBL-B / Signal transduction protein CBL-B / SH3-binding protein CBL-B / Casitas B-lineage lymphoma proto- ...Signal transduction protein CBL-B / SH3-binding protein CBL-B / Casitas B-lineage lymphoma proto-oncogene b / RING finger protein 56


Mass: 5656.381 Da / Num. of mol.: 1 / Fragment: UBA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBLB, RNF56 / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q13191, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P62990, UniProt: P0CH28*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2M calcium chloride, 0.1M sodium acetate, 20% PEG6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 20, 2006 / Details: Osmic multilayer confocal optics
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 10581 / Num. obs: 10568 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 29.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 10.9 / Num. unique all: 671 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalClear(MSC/RIGAKU)data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1UBQ, 2OOA

1ubq

2ooa


Resolution: 1.9→19.15 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.897 / SU B: 3.62 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25636 505 4.8 %RANDOM
Rwork0.19658 ---
all0.199 10581 --
obs0.199 10076 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.702 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 0 134 1058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022933
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9821253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2035114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.87925.55645
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13315186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.774156
X-RAY DIFFRACTIONr_chiral_restr0.1470.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02679
X-RAY DIFFRACTIONr_nbd_refined0.2110.2406
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2640
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2112
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.216
X-RAY DIFFRACTIONr_mcbond_it1.0421.5593
X-RAY DIFFRACTIONr_mcangle_it1.7282929
X-RAY DIFFRACTIONr_scbond_it2.8883373
X-RAY DIFFRACTIONr_scangle_it4.7774.5324
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 43 -
Rwork0.223 671 -
obs-671 90.49 %

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