PDB-2gfo: Structure of the Catalytic Domain of Human Ubiquitin Carboxyl-ter...

ID or keywords:

Entry

Database: PDB / ID: 2gfo

Title

Structure of the Catalytic Domain of Human Ubiquitin Carboxyl-terminal Hydrolase 8

Components

Ubiquitin carboxyl-terminal hydrolase 8

Keywords

HYDROLASE /

Protease /

Thiol protease / Ubl conjugation pathway /

Deubiquitinating Enzyme / DUB / Zinc ribbon /

Structural Genomics Consortium / SGC

Function / homology

Function and homology information

regulation of protein catabolic process at postsynapse, modulating synaptic transmission / negative regulation of lysosomal protein catabolic process / protein K48-linked deubiquitination / endosome organization / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / positive regulation of amyloid fibril formation /

extrinsic component of plasma membrane / protein deubiquitination ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Finerty Jr., P.J. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. ...

Citation

Journal: J.Biol.Chem. / Year: 2006
Title: Amino-terminal Dimerization, NRDP1-Rhodanese Interaction, and Inhibited Catalytic Domain Conformation of the Ubiquitin-specific Protease 8 (USP8).
Authors: Avvakumov, G.V. / Walker, J.R. / Xue, S. / Finerty Jr., P.J. / Mackenzie, F. / Newman, E.M. / Dhe-Paganon, S.

History

Deposition	Mar 22, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 4, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2gfo.cif.gz	86.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2gfo.ent.gz	69.1 KB	Display	PDB format
PDBx/mmJSON format	2gfo.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gf/2gfo ftp://data.pdbj.org/pub/pdb/validation_reports/gf/2gfo	HTTPS FTP

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Related structure data

Related structure data	2a9uC 2fzpC 2gwfC 1whb C: citing same article (ref.)
Similar structure data	6fhp-2 4e80-4 6mev-5 6wia-d 3sq3-2 4rbm-d 7js5-d 7js7-1 3d67-1 1dym-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
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (2) #234 - Jun 2019 MDM2 and Cancer similarity (2) #126 - Jun 2010 Epidermal Growth Factor similarity (1)

Deposited unit

A: Ubiquitin carboxyl-terminal hydrolase 8

hetero molecules

45.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	67.173, 67.173, 194.458
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Ubiquitin carboxyl-terminal hydrolase 8 / Ubiquitin thiolesterase 8 / Ubiquitin-specific processing protease 8 / Deubiquitinating enzyme 8 / hUBPy Mass: 45652.930 Da / Num. of mol.: 1 / Fragment: Catalytic Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP8, KIAA0055, UBPY / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P40818, EC: 3.1.2.15
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55.65 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 18% PEG3350; 0.1 M bis-Tris, pH 6.3, 0.2 M KSCN, 1 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 298, temperature 298.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97896 Å
Detector	Type: SBC-3 / Detector: CCD / Date: Mar 9, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97896 Å / Relative weight: 1
Reflection	Resolution: 2→18.2 Å / Num. all: 33281 / Num. obs: 33281 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / R_merge(I) obs: 0.085 / Net I/σ(I): 20.03
Reflection shell	Resolution: 2→2.07 Å / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling
SOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→18.2 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.947 / SU B: 6.948 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21023	1684	5.1 %	RANDOM
R_work	0.16845	-	-	-
obs	0.17056	31452	99.31 %	-
all	-	33136	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 39.287 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.12 Å²	0.56 Å²	0 Å²
2-	-	1.12 Å²	0 Å²
3-	-	-	-1.68 Å²

Refinement step

Cycle: LAST / Resolution: 2→18.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2746	0	1	191	2938

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	2810
X-RAY DIFFRACTION	r_angle_refined_deg	1.498	1.944	3789
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.855	5	337
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.312	24.184	141
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.072	15	498
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.789	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	402
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2138
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	1131
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	1901
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	165
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.127	0.2	19
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.183	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	2.245	3	1734
X-RAY DIFFRACTION	r_mcangle_it	3.078	4	2698
X-RAY DIFFRACTION	r_scbond_it	4.711	5	1237
X-RAY DIFFRACTION	r_scangle_it	6.218	7	1091

LS refinement shell

Resolution: 2→2.051 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.279	118	-
R_work	0.236	2279	-
obs	-	-	99.25 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	24.7502	-4.8687	3.9873	7.0729	-5.5014	8.3704	0.2057	0.4987	-0.9365	-0.396	-0.0937	0.6343	0.7285	-0.3733	-0.1121	0.2195	0.0062	0.0669	-0.1038	-0.0203	0.0954	10.6651	-3.1017	2.2802
2	1.7008	-0.1276	-0.0734	2.9455	0.0321	3.9002	-0.0532	-0.0593	-0.056	-0.0488	0.0526	-0.1054	0.1438	0.2011	0.0005	0.0832	0.0004	0.0415	0.037	-0.0025	0.0993	11.6052	11.0625	4.1261
3	2.5471	0.251	0.2248	2.3197	-0.6259	4.633	-0.163	0.0793	-0.2957	-0.2863	0.1285	0.2907	0.3031	-0.5207	0.0345	0.1178	-0.0256	0.0292	0.0425	0.0068	0.0787	-5.8945	8.6524	11.6145
4	2.7082	-0.8268	0.3838	1.8627	-0.7016	3.5092	-0.0954	0.1138	-0.1271	-0.0586	-0.0116	0.0671	0.191	-0.1292	0.107	0.1504	-0.0228	0.0466	0.0098	-0.0141	0.0898	3.3809	6.566	2.6265
5	2.8389	0.5188	-1.6926	0.7628	0.195	2.1101	-0.0029	0.1491	0.0871	-0.069	0.0655	0.0031	-0.1745	-0.1949	-0.0626	0.1112	0.0068	0.0168	0.0327	0.0088	0.032	-0.4709	18.0063	0.8463
6	5.4124	-14.1614	-2.6672	72.2246	15.8834	4.3131	0.0007	0.1626	-0.1931	-2.0763	-0.6588	3.6381	-0.8635	-0.9042	0.6581	0.1188	0.1712	0.0169	0.094	0.0398	0.1441	-20.7086	29.0825	13.7114
7	7.1955	2.2968	0.552	26.5811	6.7481	7.3459	-0.3754	-0.2572	0.228	0.5436	0.2513	0.6335	-0.4555	-0.622	0.1241	0.0476	0.1837	0.0796	0.0663	0.0556	0.0389	-17.2816	33.4166	19.3532
8	2.3614	1.0832	0.9747	6.0623	0.6119	2.3831	0.0488	0.084	0.027	0.2113	-0.0453	0.4344	-0.0317	-0.4127	-0.0035	0.0484	0.0378	0.0472	0.0595	0.03	0.0282	-10.3676	21.1667	14.5647
9	3.3206	-5.2665	4.9078	11.878	-8.6853	7.4842	-0.223	-0.0552	-0.0894	0.1501	0.1922	0.022	-0.1909	-0.1963	0.0308	0.1493	0.1191	0.1412	-0.0287	0.0921	0.0713	-12.1434	44.7949	7.5008
10	14.3224	-10.0433	-8.2298	13.1636	7.4513	7.9752	0.0267	0.4477	-0.1882	-0.1713	-0.0309	0.4006	-0.0274	-0.2391	0.0042	0.1312	0.0436	0.047	0.0335	0.0801	0.0232	-6.2266	29.5555	11.0313
11	6.4664	-0.7456	-1.6856	3.5455	-0.4503	2.9663	0.1279	-0.3034	0.6504	0.0485	0.1878	-0.0531	-0.7918	0.1756	-0.3156	0.1936	-0.0553	0.0787	-0.1156	-0.0248	0.1062	8.8388	38.5453	11.4078
12	25.5465	6.159	12.319	9.2222	-0.0887	7.1496	0.4208	2.7427	-0.6573	-1.111	-0.1574	-0.5778	1.6225	2.1013	-0.2634	0.408	0.33	0.3281	0.0114	0.0963	0.06	-6.5385	42.3709	-1.858
13	3.9689	-4.2438	4.7386	7.5073	-5.3309	6.4137	0.3671	0.2324	-0.0325	-0.7923	-0.2398	0.0566	0.5742	0.1782	-0.1273	0.1958	0.0783	0.1107	-0.1066	0.0208	0.0182	-12.6175	41.9923	4.9704
14	3.65	0.8872	-4.4642	1.5913	-0.7465	6.1379	0.2237	0.5438	0.3199	-0.3759	0.1243	-0.0889	-0.6816	-0.6056	-0.3479	0.1813	0.0255	0.0543	-0.0198	0.0312	0.0496	6.7303	31.4072	2.1651
15	1.9558	-1.0921	-0.4729	2.1045	-0.188	2.0993	-0.0149	-0.3976	0.2558	0.1645	0.2363	-0.1441	-0.2815	0.3042	-0.2214	0.1281	-0.0425	0.0139	-0.0529	-0.0473	0.0649	7.2544	32.8649	17.9378
16	1.843	-0.1267	-0.5604	1.9848	0.3474	2.3273	-0.0165	-0.2107	0.0362	-0.0284	0.0875	-0.2668	-0.0737	0.3554	-0.071	0.0421	-0.0182	0.0127	0.0613	-0.0188	0.0995	15.0224	19.6753	11.6985

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	762 - 770	48 - 56
2	X-RAY DIFFRACTION	2	A	A	771 - 795	57 - 81
3	X-RAY DIFFRACTION	3	A	A	796 - 822	82 - 108
4	X-RAY DIFFRACTION	4	A	A	823 - 860	109 - 146
5	X-RAY DIFFRACTION	5	A	A	861 - 885	147 - 171
6	X-RAY DIFFRACTION	6	A	A	886 - 900	172 - 186
7	X-RAY DIFFRACTION	7	A	A	901 - 913	187 - 199
8	X-RAY DIFFRACTION	8	A	A	914 - 929	200 - 215
9	X-RAY DIFFRACTION	9	A	A	930 - 945	216 - 231
10	X-RAY DIFFRACTION	10	A	A	946 - 951	232 - 237
11	X-RAY DIFFRACTION	11	A	A	952 - 973	238 - 259
12	X-RAY DIFFRACTION	12	A	A	974 - 983	260 - 269
13	X-RAY DIFFRACTION	13	A	A	984 - 1002	270 - 288
14	X-RAY DIFFRACTION	14	A	A	1003 - 1021	289 - 307
15	X-RAY DIFFRACTION	15	A	A	1022 - 1048	308 - 334
16	X-RAY DIFFRACTION	16	A	A	1049 - 1109	335 - 395

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