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- PDB-3by4: Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 3by4
TitleStructure of Ovarian Tumor (OTU) domain in complex with Ubiquitin
Components
  • Ubiquitin thioesterase OTU1
  • Ubiquitin
KeywordsCELL CYCLE / HYDROLASE / ubiquitin hydrolase / deubiquitinase
Function / homology
Function and homology information


Ovarian tumor domain proteases / : / : / protein modification process => GO:0036211 / protein deubiquitination / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency ...Ovarian tumor domain proteases / : / : / protein modification process => GO:0036211 / protein deubiquitination / 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 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / : / endoplasmic reticulum unfolded protein response / 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 / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / cytosolic ribosome / 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 / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling
Similarity search - Function
: / OTU1, UBXL domain / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Cathepsin B; Chain A / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e ...: / OTU1, UBXL domain / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Cathepsin B; Chain A / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Zinc finger C2H2 type domain signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger C2H2-type / Papain-like cysteine peptidase superfamily / 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 Complex / Alpha Beta
Similarity search - Domain/homology
3-AMINOPROPANE / Polyubiquitin-C / Ubiquitin thioesterase OTU1 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsMessick, T.E. / Marmorstein, R.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein
Authors: Messick, T.E. / Russell, N.S. / Iwata, A.J. / Sarachan, K.L. / Shiekhattar, R. / Shanks, J.R. / Reyes-Turcu, F.E. / Wilkinson, K.D. / Marmorstein, R.
History
DepositionJan 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin thioesterase OTU1
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4483
Polymers32,3892
Non-polymers591
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-12 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.304, 73.215, 88.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin thioesterase OTU1 / E.C.3.4.19.12 / Otu1 / OTU domain-containing protein 1


Mass: 23869.035 Da / Num. of mol.: 1 / Fragment: Otu domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Otu1 / Plasmid: pTYB2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P43558, ubiquitinyl hydrolase 1
#2: Protein Ubiquitin / / Ubiquitin B


Mass: 8519.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: propylamine added by intein-mediated ligation / Gene: ubiquitin B / Plasmid: pTYB2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62988, UniProt: P0CG48*PLUS
#3: Chemical ChemComp-3CN / 3-AMINOPROPANE / Propylamine


Mass: 59.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Bis-Tris, Magnesium Chloride, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.0722, 1.7025, 1.0450
SYNCHROTRONAPS 18-ID20.9795
Detector
TypeIDDetectorDate
MARRESEARCH1CCDMar 25, 2005
MARRESEARCH2CCDMar 25, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELMADMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.07221
21.70251
31.0451
40.97951
ReflectionRedundancy: 7.5 % / Av σ(I) over netI: 21.3 / Number: 295410 / Rmerge(I) obs: 0.095 / Χ2: 1.04 / D res high: 1.55 Å / D res low: 20 Å / Num. obs: 39220 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.3209910.1141.0897.8
3.424.399.910.0811.0257.2
2.993.4299.910.0741.0977.5
2.712.9910010.0771.0517.6
2.522.7199.910.081.0967.6
2.372.5210010.0881.0217.6
2.252.3710010.0991.0037.6
2.152.2510010.1281.0237.5
2.072.1510010.1371.0267.5
22.0710010.1641.0157.5
ReflectionResolution: 1.55→37.99 Å / Num. obs: 44240 / % possible obs: 99.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.037 / Χ2: 1.034 / Net I/σ(I): 31.2

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Phasing

PhasingMethod: MAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_11.5537.9900398264339
ISO_21.5537.990.2630.252321883824
ISO_31.5537.990.5840.617358374089
ANO_11.5537.991.370397780
ANO_21.5537.990.6840321760
ANO_31.5537.990.7270358580
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_16.82-37.9900375192
ISO_14.87-6.8200765224
ISO_13.98-4.87001015223
ISO_13.45-3.98001209216
ISO_13.09-3.45001394220
ISO_12.82-3.09001555220
ISO_12.62-2.82001690218
ISO_12.45-2.62001826227
ISO_12.31-2.45001963233
ISO_12.19-2.31002081223
ISO_12.09-2.19002180228
ISO_12-2.09002286230
ISO_11.92-2002392221
ISO_11.85-1.92002490217
ISO_11.79-1.85002590223
ISO_11.73-1.79002703229
ISO_11.68-1.73002757230
ISO_11.63-1.68002850227
ISO_11.59-1.63002892189
ISO_11.55-1.59002813149
ANO_16.82-37.993.07303710
ANO_14.87-6.824.41307650
ANO_13.98-4.872.91010150
ANO_13.45-3.982.374012080
ANO_13.09-3.452.221013940
ANO_12.82-3.092.073015540
ANO_12.62-2.821.864016890
ANO_12.45-2.621.574018230
ANO_12.31-2.451.268019630
ANO_12.19-2.310.964020800
ANO_12.09-2.190.76021800
ANO_12-2.090.599022850
ANO_11.92-20.485023920
ANO_11.85-1.920.361024890
ANO_11.79-1.850.291025900
ANO_11.73-1.790.24027030
ANO_11.68-1.730.197027560
ANO_11.63-1.680.171028500
ANO_11.59-1.630.132028760
ANO_11.55-1.590.116027950
ISO_26.82-37.990.6210.489375190
ISO_24.87-6.820.5290.414765223
ISO_23.98-4.870.3440.2371015221
ISO_23.45-3.980.2960.2211209210
ISO_23.09-3.450.2760.1781394217
ISO_22.82-3.090.2730.1971555220
ISO_22.62-2.820.2620.1731690217
ISO_22.45-2.620.2340.1521823227
ISO_22.31-2.450.190.1221963233
ISO_22.19-2.310.1470.1112081223
ISO_22.09-2.190.1330.0922179228
ISO_22-2.090.1090.0752286229
ISO_21.92-20.0950.0712392221
ISO_21.85-1.920.0650.0482490217
ISO_21.79-1.850.0640.052590222
ISO_21.73-1.790.0560.0352702228
ISO_21.68-1.730.0440.0322749229
ISO_21.63-1.680.0390.03293069
ISO_21.59-1.630000
ISO_21.55-1.590000
ANO_26.82-37.991.74503760
ANO_24.87-6.823.72607640
ANO_23.98-4.872.721010140
ANO_23.45-3.982.283012080
ANO_23.09-3.452.241013930
ANO_22.82-3.091.777015520
ANO_22.62-2.821.331016890
ANO_22.45-2.620.934018210
ANO_22.31-2.450.669019630
ANO_22.19-2.310.431020800
ANO_22.09-2.190.306021790
ANO_22-2.090.212022860
ANO_21.92-20.159023920
ANO_21.85-1.920.122024890
ANO_21.79-1.850.103025900
ANO_21.73-1.790.093027020
ANO_21.68-1.730.078027480
ANO_21.63-1.680.07509300
ANO_21.59-1.630000
ANO_21.55-1.590000
ISO_36.82-37.990.9691.19375188
ISO_34.87-6.822.4361.21765224
ISO_33.98-4.871.8210.9891015219
ISO_33.45-3.981.680.9951209210
ISO_33.09-3.451.6070.9421391216
ISO_32.82-3.091.4250.8591553219
ISO_32.62-2.821.2080.6881684216
ISO_32.45-2.620.9380.5631826226
ISO_32.31-2.450.7070.3841963231
ISO_32.19-2.310.510.2972081223
ISO_32.09-2.190.3870.2132180228
ISO_32-2.090.2650.1672286230
ISO_31.92-20.1980.1232392220
ISO_31.85-1.920.1410.0882490217
ISO_31.79-1.850.1130.0892590222
ISO_31.73-1.790.0910.0582702223
ISO_31.68-1.730.0710.0532755230
ISO_31.63-1.680.0560.042850226
ISO_31.59-1.630.0470.0391730121
ISO_31.55-1.590000
ANO_36.82-37.991.73903790
ANO_34.87-6.823.26607650
ANO_33.98-4.872.635010150
ANO_33.45-3.981.926012090
ANO_33.09-3.451.996013930
ANO_32.82-3.091.705015570
ANO_32.62-2.821.426016830
ANO_32.45-2.621.029018270
ANO_32.31-2.450.764019620
ANO_32.19-2.310.529020810
ANO_32.09-2.190.387021800
ANO_32-2.090.284022860
ANO_31.92-20.211023920
ANO_31.85-1.920.16024900
ANO_31.79-1.850.129025900
ANO_31.73-1.790.105027020
ANO_31.68-1.730.089027550
ANO_31.63-1.680.079028500
ANO_31.59-1.630.072017420
ANO_31.55-1.590000

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
PHENIXrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 1.55→37.99 Å / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.211 2221 5.02 %
Rwork0.189 --
obs0.191 44240 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 11.53 Å2 / Biso mean: 32.26 Å2 / Biso min: 119.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.179 Å20 Å20 Å2
2--0.313 Å2-0 Å2
3---0.465 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 4 144 2104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051992
X-RAY DIFFRACTIONf_angle_d0.8512686
X-RAY DIFFRACTIONf_chiral_restr0.056310
X-RAY DIFFRACTIONf_plane_restr0.003345
X-RAY DIFFRACTIONf_dihedral_angle_d15.297737
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.5840.2961200.2272375249590
1.584-1.6210.2771580.2052495265397
1.621-1.6610.251300.18126072737100
1.661-1.7060.2281510.16326182769100
1.706-1.7560.2191340.14926002734100
1.756-1.8130.2111320.14426102742100
1.813-1.8780.1971330.13826452778100
1.878-1.9530.1631240.13426252749100
1.953-2.0420.2021690.14426152784100
2.042-2.1490.1961500.14426172767100
2.149-2.2840.181220.15326702792100
2.284-2.460.1881320.16426582790100
2.46-2.7080.1931430.17726742817100
2.708-3.0990.2341180.226942812100
3.099-3.9050.1951430.19127012844100
3.905-38.0010.2051620.2162815297799

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