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- PDB-3a33: UbcH5b~Ubiquitin Conjugate -

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Basic information

Entry
Database: PDB / ID: 3a33
TitleUbcH5b~Ubiquitin Conjugate
Components
  • Ubiquitin-conjugating enzyme E2 D2
  • Ubiquitin
KeywordsLIGASE / E2 ubiquitin-conjugating enzyme / ubiquitin / Ubl conjugation pathway / Isopeptide bond / Nucleus
Function / homology
Function and homology information


: / : / protein modification process => GO:0036211 / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination ...: / : / protein modification process => GO:0036211 / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein K48-linked ubiquitination / protein autoubiquitination / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / cytosolic ribosome / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ribosomal L40e family ...Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSakata, E. / Satoh, T. / Yamamoto, S. / Yamaguchi, Y. / Yagi-Utsumi, M. / Kurimoto, E. / Wakatsuki, S. / Kato, K.
CitationJournal: Structure / Year: 2010
Title: Crystal Structure of UbcH5b~Ubiquitin Intermediate: Insight into the Formation of the Self-Assembled E2~Ub Conjugates
Authors: Sakata, E. / Satoh, T. / Yamamoto, S. / Yamaguchi, Y. / Yagi-Utsumi, M. / Kurimoto, E. / Tanaka, K. / Wakatsuki, S. / Kato, K.
History
DepositionJun 8, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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 / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6233
Polymers25,5312
Non-polymers921
Water1,11762
1
A: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin
hetero molecules

A: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2476
Polymers51,0624
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
Unit cell
Length a, b, c (Å)72.5, 72.5, 176.6
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsTHE UBCH5B (CHAIN A)~UBIQUITIN (CHAIN B) CONJUGATE ASSEMBLED INTO HETEROTETRAMER OR HIGHER OLIGOMERIC SPIRAL THROUGH A NON-COVALENT INTERACTION AS SHOWN IN REMARK 350.

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin-protein ligase D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2-17 kDa ...Ubiquitin-protein ligase D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / E2(17)KB 2


Mass: 16954.371 Da / Num. of mol.: 1 / Mutation: C85S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBCH5B / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon-plus / References: UniProt: P62837, ubiquitin-protein ligase
#2: Protein Ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid details: Delete GST gene in the vector / Plasmid: pGEX6P-1 (Modified) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon-plus / References: UniProt: P62988, UniProt: P0CG48*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC85S IN ENTITY 1 (CHAIN A) IS MUTATION. ENTITY 1 (UBCH5B) CONJUGATED ENTITY 2 (UB) VIA RESIDUE 85 ...C85S IN ENTITY 1 (CHAIN A) IS MUTATION. ENTITY 1 (UBCH5B) CONJUGATED ENTITY 2 (UB) VIA RESIDUE 85 SER OF CHAIN A AND RESIDUE 76 GLY OF CHAIN B.

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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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 2.0M NaCl, 0.1M Potassium acetate, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 14779 / Num. obs: 14712 / % possible obs: 99.6 % / Redundancy: 12 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 47.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1388 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ESK and 1UBQ

2esk

1ubq


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.5 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28 735 5 %RANDOM
Rwork0.228 ---
all0.231 13874 --
obs0.231 13874 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.641 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20.69 Å20 Å2
2--1.38 Å20 Å2
3----2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 6 62 1862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221851
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9762511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22724.14682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.16715323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7571512
X-RAY DIFFRACTIONr_chiral_restr0.0990.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021398
X-RAY DIFFRACTIONr_nbd_refined0.1890.2782
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21268
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.214
X-RAY DIFFRACTIONr_mcbond_it0.921.51171
X-RAY DIFFRACTIONr_mcangle_it1.62521855
X-RAY DIFFRACTIONr_scbond_it2.3173768
X-RAY DIFFRACTIONr_scangle_it3.7124.5655
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 41 -
Rwork0.252 968 -
obs--96.46 %

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