PDB-8itp: Crystal structure of USP47 catalytic domain complex with ubiquitin

ID or keywords:

Entry

Database: PDB / ID: 8itp

Title

Crystal structure of USP47 catalytic domain complex with ubiquitin

Components

Ubiquitin
Ubiquitin carboxyl-terminal hydrolase 47

Keywords

HYDROLASE/INHIBITOR / Ubiquitin specific protease / HYDROLASE-INHIBITOR COMPLEX

Function / homology

Function and homology information

anterior/posterior axis specification, embryo / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / protein deubiquitination / regulation of protein stability / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / proteolysis / metal ion binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Caenorhabditis elegans (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Kim, E.E. / Shin, S.C.

Funding support

Korea, Republic Of, 1items

Citation

Journal: Commun Biol / Year: 2023
Title: Structural and functional characterization of USP47 reveals a hot spot for inhibitor design.
Authors: Shin, S.C. / Park, J. / Kim, K.H. / Yoon, J.M. / Cho, J. / Ha, B.H. / Oh, Y. / Choo, H. / Song, E.J. / Kim, E.E.

History

Deposition	Mar 22, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 27, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Database references / Category: citation Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8itp.cif.gz	356.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8itp.ent.gz	292.5 KB	Display	PDB format
PDBx/mmJSON format	8itp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8itp_validation.pdf.gz	966.2 KB	Display	wwPDB validaton report
Full document	8itp_full_validation.pdf.gz	980.6 KB	Display
Data in XML	8itp_validation.xml.gz	30.6 KB	Display
Data in CIF	8itp_validation.cif.gz	40.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/it/8itp ftp://data.pdbj.org/pub/pdb/validation_reports/it/8itp	HTTPS FTP

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Related structure data

Related structure data	8itnC C: citing same article (ref.)
Similar structure data	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	#234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

C: Ubiquitin

D: Ubiquitin carboxyl-terminal hydrolase 47

A: Ubiquitin

B: Ubiquitin carboxyl-terminal hydrolase 47

hetero molecules

132 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: Ubiquitin

D: Ubiquitin carboxyl-terminal hydrolase 47

hetero molecules

defined by author&software
66.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Ubiquitin

B: Ubiquitin carboxyl-terminal hydrolase 47

hetero molecules

defined by author&software
66.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	46.957, 93.399, 217.762
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Ubiquitin Mass: 8576.831 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#2: Protein	Ubiquitin carboxyl-terminal hydrolase 47 / Ubiquitin thioesterase 47 / Ubiquitin-specific-processing protease 47 Mass: 57567.887 Da / Num. of mol.: 2 / Mutation: C97S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_T05H10.1, T05H10.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q22240, ubiquitinyl hydrolase 1
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.8 Å³/Da / Density % sol: 31.85 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM bis-Tris (pH 5.5), 25% PEG 3350, 50 mM MgCl2 PH range: 4.5 - 6.5

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Data collection

Diffraction

Mean temperature: 298 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 5C (4A) / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 21, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 3→50 Å / Num. obs: 19209 / % possible obs: 96.4 % / Redundancy: 4.2 % / R_merge(I) obs: 0.14 / Χ²: 0.915 / Net I/σ(I): 6.6 / Num. measured all: 80505

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
3-3.11	2.8	0.374	1776	0.842	1	91.4
3.11-3.23	3	0.351	1820	0.862	1	94.4
3.23-3.38	3.5	0.314	1902	0.837	1	96.1
3.38-3.56	3.9	0.277	1880	0.902	1	97.3
3.56-3.78	4.2	0.246	1917	0.988	1	97.7
3.78-4.07	4.4	0.186	1920	1.009	1	97.3
4.07-4.48	4.6	0.138	1940	1.117	1	97.6
4.48-5.13	5	0.105	1964	0.996	1	97.8
5.13-6.46	5	0.099	1997	0.845	1	98.1
6.46-50	5.3	0.066	2093	0.728	1	96.1

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
HKL-2000		data reduction
PHENIX	1.20.1-4487	refinement
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3→29.51 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 28.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2843	1756	10 %
R_work	0.2461	-	-
obs	0.25	17554	87.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3→29.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6771	0	2	0	6773

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6907
X-RAY DIFFRACTION	f_angle_d	0.45	9325
X-RAY DIFFRACTION	f_dihedral_angle_d	12.15	2583
X-RAY DIFFRACTION	f_chiral_restr	0.037	1022
X-RAY DIFFRACTION	f_plane_restr	0.004	1208

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3-3.08	0.368	72	0.3432	646	X-RAY DIFFRACTION	48
3.08-3.17	0.387	93	0.3342	835	X-RAY DIFFRACTION	62
3.17-3.28	0.3462	111	0.3439	1010	X-RAY DIFFRACTION	75
3.28-3.39	0.3663	132	0.3034	1182	X-RAY DIFFRACTION	86
3.39-3.53	0.3013	135	0.3066	1215	X-RAY DIFFRACTION	91
3.53-3.69	0.3145	146	0.2849	1313	X-RAY DIFFRACTION	95
3.69-3.88	0.3127	148	0.2586	1328	X-RAY DIFFRACTION	97
3.88-4.12	0.2691	146	0.266	1319	X-RAY DIFFRACTION	97
4.12-4.44	0.2777	150	0.223	1352	X-RAY DIFFRACTION	98
4.44-4.89	0.2741	150	0.2085	1350	X-RAY DIFFRACTION	98
4.89-5.59	0.2672	153	0.223	1366	X-RAY DIFFRACTION	98
5.59-7.03	0.3071	156	0.2455	1411	X-RAY DIFFRACTION	98
7.03-29.51	0.2229	164	0.203	1471	X-RAY DIFFRACTION	98

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	6.6787	-1.2609	-1.369	2.2461	-1.1668	6.194	0.361	-0.2393	-0.0604	-0.2707	0.5871	0.5532	-0.0965	-0.8128	0.8356	0.3958	0.3523	-0.4372	0.949	-0.4221	0.9717	58.363	210.451	34.3313
2	4.7741	-1.313	-1.6796	2.5833	2.7599	2.9678	-0.0369	0.3505	0.2545	-0.1619	-0.5625	0.4433	0.3456	-0.3425	0.316	0.7723	0.4347	0.1951	0.9428	-0.3001	0.8157	58.5805	214.7685	31.4573
3	2.5001	1.5432	1.5582	3.7385	0.0121	1.3529	0.3649	0.1566	1.1638	0.3533	-1.3106	0.3042	0.0873	-0.0132	0.8665	0.9772	-0.0062	-0.0356	0.7224	0.021	0.7012	65.6486	224.6955	36.7133
4	1.8681	0.0525	-1.1879	3.3227	-0.3294	1.5638	0.4423	0.7843	0.6343	-0.2447	-0.4457	0.9024	-0.2004	-0.5898	0.2581	1.1288	0.9446	-0.2484	1.0279	-0.3765	0.8978	54.8941	220.0045	39.1604
5	5.4466	-3.4813	2.0291	7.0742	-2.3319	3.2471	1.0899	0.1409	0.5432	0.0779	-0.4349	-0.0965	-0.0612	-1.8081	-0.0367	0.7841	0.064	0.0268	0.981	-0.3276	1.0231	53.763	215.1282	45.9021
6	6.9596	1.9752	4.2073	3.8933	3.3211	9.3039	0.4762	0.3762	0.7062	0.4782	-0.189	-1.0835	-0.4815	-0.2179	0.2963	0.6391	0.1484	-0.0345	0.6026	-0.0875	0.678	67.9945	216.5516	42.5861
7	1.3501	0.8831	-2.3324	4.0993	-0.8219	4.0933	0.0848	-0.2775	-0.386	1.0519	0.0052	0.1611	-0.528	0.218	-0.1533	0.5458	0.3408	0.1961	1.0785	-0.0785	0.5559	55.3241	209.9118	47.395
8	2.0017	0.3411	1.1395	5.8843	-1.8507	4.4773	-0.0503	-0.5029	-0.1942	-0.376	-1.1598	0.3242	0.7717	0.1189	0.2298	0.6507	0.0241	0.1754	0.7396	0.0413	0.5128	57.8219	196.872	69.6773
9	3.5129	2.0809	1.0049	5.2423	2.2586	5.6784	0.0044	-0.5574	0.5282	0.5519	-0.412	0.1442	-0.3751	0.0929	0.3497	0.5592	0.2652	-0.0035	0.701	0.0508	0.5482	66.3419	204.9508	70.3723
10	4.5769	2.8305	0.8602	5.2285	2.5548	7.1243	0.1129	0.5046	0.1951	-0.8326	-0.1418	-0.0549	-0.2697	0.5045	0.2074	0.5412	0.0923	0.0007	0.6347	0.1804	0.4394	72.6693	206.2666	57.4515
11	1.0034	-0.8426	0.0874	1.5298	0.651	2.4438	-0.3515	-0.002	-0.1937	-0.0512	-0.0033	-0.3675	-0.0713	-0.7328	0.359	0.3315	-0.0373	0.0496	0.5474	-0.1185	0.5366	61.6098	202.7158	31.6164
12	3.7798	0.5491	0.4484	2.0799	0.6556	2.054	-0.2688	-0.4296	-0.7865	-0.6081	0.2501	0.1952	0.4983	-0.8011	0.1588	0.5645	-0.1412	0.09	0.7483	0.0366	0.5003	54.0531	194.6899	46.8377
13	2.6418	0.4846	1.1718	1.2553	0.8757	1.4081	-0.2168	-0.213	-0.5156	0.4485	0.2344	-0.0888	0.2041	-0.3617	-0.162	0.6195	0.0019	0.2724	0.5221	0.1189	0.6243	59.57	189.6187	58.9201
14	2.9028	-1.8683	0.5218	1.9122	-0.3734	2.789	-0.1152	-0.035	-0.0913	0.0938	0.4009	0.1988	0.2992	1.2696	-0.5791	-0.3676	0.3324	-0.0592	0.8992	-0.1847	0.499	41.8811	205.5099	15.631
15	1.3591	0.9346	0.9184	0.8074	-0.1955	4.8233	-0.5162	-0.4772	0.9138	0.213	-0.1981	0.3677	-1.0281	0.1971	0.2971	0.37	-0.0725	-0.2538	0.7083	-0.3051	0.6793	41.8123	210.4865	15.9797
16	9.8314	-0.3079	2.9759	0.7041	-1.8921	5.5611	-0.4785	0.0183	1.0236	0.0542	-0.3632	0.1125	-0.8429	-0.002	0.7269	0.3962	0.2439	-0.1889	0.4745	-0.1174	0.5645	34.9257	216.3565	6.2312
17	5.3163	-0.3352	0.3852	5.1654	0.7692	6.9097	-0.4737	-0.145	0.7618	-0.2535	-0.6121	-0.0937	0.2218	1.2579	1.053	0.4983	-0.0917	-0.0853	0.3129	0.2877	0.6359	45.4927	210.9658	6.7978
18	5.5837	2.5261	0.0379	4.626	-2.312	3.6455	0.2346	0.1969	-0.1187	-0.3414	0.3422	-0.6717	0.7086	0.171	-0.1525	0.2102	0.0872	0.0207	0.5879	-0.042	0.4668	42.2937	201.9721	4.0309
19	5.8069	0.5432	-4.3357	5.303	1.9503	7.1418	0.5438	0.5433	-0.081	-0.1996	0.3073	0.3279	0.0166	-0.3856	-0.5836	0.3174	0.1066	0.2409	0.3346	-0.1479	0.623	32.024	208.2073	5.7948
20	4.8685	0.604	1.6476	2.439	-0.4112	2.5393	-0.4037	1.236	-0.7591	-0.2398	-0.5273	-0.989	0.1827	0.6058	0.1123	0.4318	0.0599	-0.1179	0.5134	0.0106	0.6917	44.9545	198.4224	4.8559
21	1.3999	-0.5486	-0.4041	1.6878	0.747	2.6449	-0.1945	0.0246	0.0114	-0.1603	-0.0622	0.1545	0.14	-0.0729	0.1806	0.2981	-0.0496	0.0189	0.2961	0.0655	0.3228	36.2885	189.7494	3.5417
22	1.7976	-0.1751	-0.135	1.1836	-0.2672	2.4745	-0.1899	-0.1758	-0.3696	0.1632	0.0837	-0.1797	0.9802	0.3444	0.0299	0.8114	0.1169	0.1076	0.3225	0.1065	0.4625	43.1958	178.1439	7.4011

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 1 through 11 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 12 through 16 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 17 through 22 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 23 through 34 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 35 through 44 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 45 through 65 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 66 through 75 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 78 through 106 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 107 through 180 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 181 through 208 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 209 through 288 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 289 through 389 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 390 through 492 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 1 through 11 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 12 through 16 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 17 through 22 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 23 through 34 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 35 through 49 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 50 through 65 )
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 66 through 75 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 78 through 298 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 299 through 492 )

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