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

ID or keywords:

Entry

Database: PDB / ID: 3by4

Title

Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin

Components

Ubiquitin
Ubiquitin thioesterase OTU1

Keywords

CELL CYCLE / HYDROLASE / ubiquitin hydrolase / deubiquitinase

Function / homology

Function and homology information

Ovarian tumor domain proteases / : / : / protein modification process => GO:0036211 / 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 ...Ovarian tumor domain proteases / : / : / protein modification process => GO:0036211 / 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 / protein deubiquitination / 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 / ERAD pathway / Maturation of protein E / Maturation of protein E / cytosolic ribosome / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / 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 / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / 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 / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 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 / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.55 Å

Authors

Messick, T.E. / Marmorstein, R.

Citation

Journal: 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

Deposition	Jan 15, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 19, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Mar 26, 2025	Group: 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 / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/by/3by4 ftp://data.pdbj.org/pub/pdb/validation_reports/by/3by4	HTTPS FTP

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Related structure data

Related structure data	3c0rC C: citing same article (ref.)
Similar structure data	1gij-d 3c0r-1 3c0r-2 3en6-2 2w17-d 6q4j-d 3sw7-d 1oit-d 2w06-d 2x8e-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: Ubiquitin thioesterase OTU1

B: Ubiquitin

hetero molecules

32.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

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 number	19
Space group name H-M	P2₁2₁2₁

#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 Mass: 59.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₉N
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 47.05 %
Crystal grow	Temperature: 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

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	19-ID	1	1.0722, 1.7025, 1.0450
SYNCHROTRON	APS	18-ID	2	0.9795

Detector

Type	ID	Detector	Date
MARRESEARCH	1	CCD	Mar 25, 2005
MARRESEARCH	2	CCD	Mar 25, 2005

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si 111 CHANNEL	MAD	M	x-ray	1
2	Si 111 CHANNEL	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.0722	1
2	1.7025	1
3	1.045	1
4	0.9795	1

Reflection

Redundancy: 7.5 % / Av σ(I) over netI: 21.3 / Number: 295410 / R_merge(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 (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.3	20	99	1	0.114	1.089	7.8
3.42	4.3	99.9	1	0.081	1.025	7.2
2.99	3.42	99.9	1	0.074	1.097	7.5
2.71	2.99	100	1	0.077	1.051	7.6
2.52	2.71	99.9	1	0.08	1.096	7.6
2.37	2.52	100	1	0.088	1.021	7.6
2.25	2.37	100	1	0.099	1.003	7.6
2.15	2.25	100	1	0.128	1.023	7.5
2.07	2.15	100	1	0.137	1.026	7.5
2	2.07	100	1	0.164	1.015	7.5

Reflection

Resolution: 1.55→37.99 Å / Num. obs: 44240 / % possible obs: 99.2 % / Redundancy: 6.6 % / R_merge(I) obs: 0.037 / Χ²: 1.034 / Net I/σ(I): 31.2

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Phasing

Phasing

Method:

MAD

Phasing MAD set

ID	Highest resolution (Å)	Lowest resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	1.55	37.99	0	0	39826	4339
ISO_2	1.55	37.99	0.263	0.252	32188	3824
ISO_3	1.55	37.99	0.584	0.617	35837	4089
ANO_1	1.55	37.99	1.37	0	39778	0
ANO_2	1.55	37.99	0.684	0	32176	0
ANO_3	1.55	37.99	0.727	0	35858	0

Phasing MAD set shell

ID	Resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	6.82-37.99	0	0	375	192
ISO_1	4.87-6.82	0	0	765	224
ISO_1	3.98-4.87	0	0	1015	223
ISO_1	3.45-3.98	0	0	1209	216
ISO_1	3.09-3.45	0	0	1394	220
ISO_1	2.82-3.09	0	0	1555	220
ISO_1	2.62-2.82	0	0	1690	218
ISO_1	2.45-2.62	0	0	1826	227
ISO_1	2.31-2.45	0	0	1963	233
ISO_1	2.19-2.31	0	0	2081	223
ISO_1	2.09-2.19	0	0	2180	228
ISO_1	2-2.09	0	0	2286	230
ISO_1	1.92-2	0	0	2392	221
ISO_1	1.85-1.92	0	0	2490	217
ISO_1	1.79-1.85	0	0	2590	223
ISO_1	1.73-1.79	0	0	2703	229
ISO_1	1.68-1.73	0	0	2757	230
ISO_1	1.63-1.68	0	0	2850	227
ISO_1	1.59-1.63	0	0	2892	189
ISO_1	1.55-1.59	0	0	2813	149
ANO_1	6.82-37.99	3.073	0	371	0
ANO_1	4.87-6.82	4.413	0	765	0
ANO_1	3.98-4.87	2.91	0	1015	0
ANO_1	3.45-3.98	2.374	0	1208	0
ANO_1	3.09-3.45	2.221	0	1394	0
ANO_1	2.82-3.09	2.073	0	1554	0
ANO_1	2.62-2.82	1.864	0	1689	0
ANO_1	2.45-2.62	1.574	0	1823	0
ANO_1	2.31-2.45	1.268	0	1963	0
ANO_1	2.19-2.31	0.964	0	2080	0
ANO_1	2.09-2.19	0.76	0	2180	0
ANO_1	2-2.09	0.599	0	2285	0
ANO_1	1.92-2	0.485	0	2392	0
ANO_1	1.85-1.92	0.361	0	2489	0
ANO_1	1.79-1.85	0.291	0	2590	0
ANO_1	1.73-1.79	0.24	0	2703	0
ANO_1	1.68-1.73	0.197	0	2756	0
ANO_1	1.63-1.68	0.171	0	2850	0
ANO_1	1.59-1.63	0.132	0	2876	0
ANO_1	1.55-1.59	0.116	0	2795	0
ISO_2	6.82-37.99	0.621	0.489	375	190
ISO_2	4.87-6.82	0.529	0.414	765	223
ISO_2	3.98-4.87	0.344	0.237	1015	221
ISO_2	3.45-3.98	0.296	0.221	1209	210
ISO_2	3.09-3.45	0.276	0.178	1394	217
ISO_2	2.82-3.09	0.273	0.197	1555	220
ISO_2	2.62-2.82	0.262	0.173	1690	217
ISO_2	2.45-2.62	0.234	0.152	1823	227
ISO_2	2.31-2.45	0.19	0.122	1963	233
ISO_2	2.19-2.31	0.147	0.111	2081	223
ISO_2	2.09-2.19	0.133	0.092	2179	228
ISO_2	2-2.09	0.109	0.075	2286	229
ISO_2	1.92-2	0.095	0.071	2392	221
ISO_2	1.85-1.92	0.065	0.048	2490	217
ISO_2	1.79-1.85	0.064	0.05	2590	222
ISO_2	1.73-1.79	0.056	0.035	2702	228
ISO_2	1.68-1.73	0.044	0.032	2749	229
ISO_2	1.63-1.68	0.039	0.032	930	69
ISO_2	1.59-1.63	0	0	0	0
ISO_2	1.55-1.59	0	0	0	0
ANO_2	6.82-37.99	1.745	0	376	0
ANO_2	4.87-6.82	3.726	0	764	0
ANO_2	3.98-4.87	2.721	0	1014	0
ANO_2	3.45-3.98	2.283	0	1208	0
ANO_2	3.09-3.45	2.241	0	1393	0
ANO_2	2.82-3.09	1.777	0	1552	0
ANO_2	2.62-2.82	1.331	0	1689	0
ANO_2	2.45-2.62	0.934	0	1821	0
ANO_2	2.31-2.45	0.669	0	1963	0
ANO_2	2.19-2.31	0.431	0	2080	0
ANO_2	2.09-2.19	0.306	0	2179	0
ANO_2	2-2.09	0.212	0	2286	0
ANO_2	1.92-2	0.159	0	2392	0
ANO_2	1.85-1.92	0.122	0	2489	0
ANO_2	1.79-1.85	0.103	0	2590	0
ANO_2	1.73-1.79	0.093	0	2702	0
ANO_2	1.68-1.73	0.078	0	2748	0
ANO_2	1.63-1.68	0.075	0	930	0
ANO_2	1.59-1.63	0	0	0	0
ANO_2	1.55-1.59	0	0	0	0
ISO_3	6.82-37.99	0.969	1.19	375	188
ISO_3	4.87-6.82	2.436	1.21	765	224
ISO_3	3.98-4.87	1.821	0.989	1015	219
ISO_3	3.45-3.98	1.68	0.995	1209	210
ISO_3	3.09-3.45	1.607	0.942	1391	216
ISO_3	2.82-3.09	1.425	0.859	1553	219
ISO_3	2.62-2.82	1.208	0.688	1684	216
ISO_3	2.45-2.62	0.938	0.563	1826	226
ISO_3	2.31-2.45	0.707	0.384	1963	231
ISO_3	2.19-2.31	0.51	0.297	2081	223
ISO_3	2.09-2.19	0.387	0.213	2180	228
ISO_3	2-2.09	0.265	0.167	2286	230
ISO_3	1.92-2	0.198	0.123	2392	220
ISO_3	1.85-1.92	0.141	0.088	2490	217
ISO_3	1.79-1.85	0.113	0.089	2590	222
ISO_3	1.73-1.79	0.091	0.058	2702	223
ISO_3	1.68-1.73	0.071	0.053	2755	230
ISO_3	1.63-1.68	0.056	0.04	2850	226
ISO_3	1.59-1.63	0.047	0.039	1730	121
ISO_3	1.55-1.59	0	0	0	0
ANO_3	6.82-37.99	1.739	0	379	0
ANO_3	4.87-6.82	3.266	0	765	0
ANO_3	3.98-4.87	2.635	0	1015	0
ANO_3	3.45-3.98	1.926	0	1209	0
ANO_3	3.09-3.45	1.996	0	1393	0
ANO_3	2.82-3.09	1.705	0	1557	0
ANO_3	2.62-2.82	1.426	0	1683	0
ANO_3	2.45-2.62	1.029	0	1827	0
ANO_3	2.31-2.45	0.764	0	1962	0
ANO_3	2.19-2.31	0.529	0	2081	0
ANO_3	2.09-2.19	0.387	0	2180	0
ANO_3	2-2.09	0.284	0	2286	0
ANO_3	1.92-2	0.211	0	2392	0
ANO_3	1.85-1.92	0.16	0	2490	0
ANO_3	1.79-1.85	0.129	0	2590	0
ANO_3	1.73-1.79	0.105	0	2702	0
ANO_3	1.68-1.73	0.089	0	2755	0
ANO_3	1.63-1.68	0.079	0	2850	0
ANO_3	1.59-1.63	0.072	0	1742	0
ANO_3	1.55-1.59	0	0	0	0

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
SOLOMON		phasing
PHENIX		refinement
PDB_EXTRACT	3.004	data extraction
HKL-2000		data collection

Refinement

Method to determine structure:

MAD / Resolution: 1.55→37.99 Å / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.211	2221	5.02 %
R_work	0.189	-	-
obs	0.191	44240	99.13 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 11.53 Å² / B_iso mean: 32.26 Å² / B_iso min: 119.6 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.179 Å²	0 Å²	0 Å²
2-	-	0.313 Å²	-0 Å²
3-	-	-	0.465 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→37.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1956	0	4	144	2104

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	1992
X-RAY DIFFRACTION	f_angle_d	0.851	2686
X-RAY DIFFRACTION	f_chiral_restr	0.056	310
X-RAY DIFFRACTION	f_plane_restr	0.003	345
X-RAY DIFFRACTION	f_dihedral_angle_d	15.297	737

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.55-1.584	0.296	120	0.227	2375	2495	90
1.584-1.621	0.277	158	0.205	2495	2653	97
1.621-1.661	0.25	130	0.181	2607	2737	100
1.661-1.706	0.228	151	0.163	2618	2769	100
1.706-1.756	0.219	134	0.149	2600	2734	100
1.756-1.813	0.211	132	0.144	2610	2742	100
1.813-1.878	0.197	133	0.138	2645	2778	100
1.878-1.953	0.163	124	0.134	2625	2749	100
1.953-2.042	0.202	169	0.144	2615	2784	100
2.042-2.149	0.196	150	0.144	2617	2767	100
2.149-2.284	0.18	122	0.153	2670	2792	100
2.284-2.46	0.188	132	0.164	2658	2790	100
2.46-2.708	0.193	143	0.177	2674	2817	100
2.708-3.099	0.234	118	0.2	2694	2812	100
3.099-3.905	0.195	143	0.191	2701	2844	100
3.905-38.001	0.205	162	0.216	2815	2977	99

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