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- PDB-4dhz: The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub -

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Basic information

Entry
Database: PDB / ID: 4dhz
TitleThe structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub
Components
  • Ubiquitin
  • Ubiquitin aldehyde
  • Ubiquitin thioesterase otubain-like
  • Ubiquitin-conjugating enzyme E2 N
KeywordsHYDROLASE/SIGNALING PROTEIN/LIGASE / ubiquitination / HYDROLASE-SIGNALING PROTEIN-LIGASE complex
Function / homology
Function and homology information


Ovarian tumor domain proteases / negative regulation of double-strand break repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase inhibitor activity / ubiquitin-protein transferase activator activity / deNEDDylase activity / positive regulation of protein K63-linked ubiquitination / protein K48-linked deubiquitination / DNA double-strand break processing ...Ovarian tumor domain proteases / negative regulation of double-strand break repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase inhibitor activity / ubiquitin-protein transferase activator activity / deNEDDylase activity / positive regulation of protein K63-linked ubiquitination / protein K48-linked deubiquitination / DNA double-strand break processing / DNA damage tolerance / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / protein deubiquitination / protein monoubiquitination / ubiquitin ligase complex / regulation of DNA repair / negative regulation of TORC1 signaling / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / antiviral innate immune response / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / positive regulation of TORC1 signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / positive regulation of DNA repair / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Downregulation of TGF-beta receptor signaling / ubiquitin binding / Josephin domain DUBs / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A
Similarity search - Function
Ubiquitin thioesterase Otubain / Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. ...Ubiquitin thioesterase Otubain / Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Phosphorylase Kinase; domain 1 / Roll / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 N / Ubiquitin thioesterase OTUB1 / Ubiquitin thioesterase otubain-like
Similarity search - Component
Biological speciesHomo sapiens (human)
Caenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsWiener, R. / Zhang, X. / Wang, T. / Wolberger, C.
CitationJournal: Nature / Year: 2012
Title: The mechanism of OTUB1-mediated inhibition of ubiquitination.
Authors: Wiener, R. / Zhang, X. / Wang, T. / Wolberger, C.
History
DepositionJan 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Mar 14, 2012Group: Database references
Revision 1.3Apr 4, 2012Group: Database references
Revision 1.4Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.5Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Mar 26, 2025Group: 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_label_atom_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin thioesterase otubain-like
B: Ubiquitin aldehyde
E: Ubiquitin
F: Ubiquitin-conjugating enzyme E2 N


Theoretical massNumber of molelcules
Total (without water)67,1374
Polymers67,1374
Non-polymers00
Water00
1
A: Ubiquitin thioesterase otubain-like
B: Ubiquitin aldehyde
F: Ubiquitin-conjugating enzyme E2 N


Theoretical massNumber of molelcules
Total (without water)58,5143
Polymers58,5143
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-18 kcal/mol
Surface area23140 Å2
MethodPISA
2
E: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,6231
Polymers8,6231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.371, 123.371, 68.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Ubiquitin thioesterase otubain-like / Deubiquitinating enzyme OTUB1 / OTU domain-containing ubiquitin aldehyde-binding protein 1 / ...Deubiquitinating enzyme OTUB1 / OTU domain-containing ubiquitin aldehyde-binding protein 1 / Otubain-1 / hOTU1 / Ubiquitin-specific-processing protease OTUB1 / Deubiquitinating enzyme otubain-like / Ubiquitin-specific-processing protease otubain-like


Mass: 32795.637 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Caenorhabditis elegans (invertebrata)
Gene: OTUB1, OTB1, OTU1, HSPC263, C25D7.8, otub-1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96FW1, UniProt: Q9XVR6, ubiquitinyl hydrolase 1
#2: Protein Ubiquitin aldehyde


Mass: 8560.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Protein Ubiquitin


Mass: 8622.922 Da / Num. of mol.: 1 / Mutation: G76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#4: Protein Ubiquitin-conjugating enzyme E2 N / Ubc13 / Bendless-like ubiquitin-conjugating enzyme / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17157.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli (E. coli) / References: UniProt: P61088, ubiquitin-protein ligase
Has protein modificationY
Sequence detailsTHE UBIQUITIN THIOESTERASE CONSTRUCT IS A CHIMERA COMPRISING RESIDUES 1-45 OF UNP Q96FW1 AND ...THE UBIQUITIN THIOESTERASE CONSTRUCT IS A CHIMERA COMPRISING RESIDUES 1-45 OF UNP Q96FW1 AND RESIDUES 42-284 OF UNP Q9XVR6.

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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: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 21% PEG10000, 0.1 M sodium chloride, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2011
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.1→123.371 Å / Num. all: 18744 / Num. obs: 18369 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→45.884 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.874 / SU B: 20.913 / SU ML: 0.377 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28768 940 5.1 %RANDOM
Rwork0.23266 ---
obs0.2356 17369 97.52 %-
all-18369 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.403 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 3.11→45.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 0 0 4370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224460
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.9716052
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.825548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35224.515206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.08415774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9291528
X-RAY DIFFRACTIONr_chiral_restr0.0790.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213366
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5181.52763
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97224464
X-RAY DIFFRACTIONr_scbond_it0.92731697
X-RAY DIFFRACTIONr_scangle_it1.7124.51588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.11→3.192 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 66 -
Rwork0.293 1161 -
obs--90.22 %

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