PDB-6h4j: Usp25 catalytic domain

ID or keywords:

Entry

Database: PDB / ID: 6h4j

Title

Usp25 catalytic domain

Components

Ubiquitin carboxyl-terminal hydrolase 25

Keywords

HYDROLASE /

Ubiquitin /

Deubiquitinase / Usp /

Cancer

Function / homology

Function and homology information

ubiquitin-like protein peptidase activity / negative regulation of ERAD pathway /

SUMO binding / protein K48-linked deubiquitination / protein K63-linked deubiquitination / protein deubiquitination /

ubiquitin binding / protein modification process /

regulation of protein stability /

peptidase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.07 Å

Authors

Klemm, T.A. / Sauer, F. / Kisker, C.

Funding support

Germany, 1items

Citation

Journal: Mol.Cell / Year: 2019
Title: Differential Oligomerization of the Deubiquitinases USP25 and USP28 Regulates Their Activities.
Authors: Sauer, F. / Klemm, T. / Kollampally, R.B. / Tessmer, I. / Nair, R.K. / Popov, N. / Kisker, C.

History

Deposition	Jul 21, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 10, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	May 15, 2019	Group: Data collection / Database references Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc Item: _citation.journal_volume / _citation.page_first
Revision 1.3	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6h4j.cif.gz	401.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6h4j.ent.gz	330.4 KB	Display	PDB format
PDBx/mmJSON format	6h4j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h4/6h4j ftp://data.pdbj.org/pub/pdb/validation_reports/h4/6h4j	HTTPS FTP

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Related structure data

Related structure data	6h4hC 6h4iSC 6h4kC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5o71-1 3lmm-d 7kfh-d 5v8m-d 6hel-1 5zny-d 3ro6-d 6kxg-d Search similar-shape structures by Omokage search (details) 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 (1) #166 - Oct 2013 Proteasome similarity (2) #81 - Sep 2006 Elongation Factors similarity (1)

Deposited unit

A: Ubiquitin carboxyl-terminal hydrolase 25

B: Ubiquitin carboxyl-terminal hydrolase 25

hetero molecules

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

1

A: Ubiquitin carboxyl-terminal hydrolase 25

hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase 25

hetero molecules

B: Ubiquitin carboxyl-terminal hydrolase 25

hetero molecules

B: Ubiquitin carboxyl-terminal hydrolase 25

hetero molecules

defined by author&software
Evidence: light scattering, SEC MALS homotetramer
257 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	81.945, 202.629, 169.594
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Ubiquitin carboxyl-terminal hydrolase 25 / Deubiquitinating enzyme 25 / USP on chromosome 21 / Ubiquitin thioesterase 25 / Ubiquitin-specific- ...Deubiquitinating enzyme 25 / USP on chromosome 21 / Ubiquitin thioesterase 25 / Ubiquitin-specific-processing protease 25 Mass: 64199.180 Da / Num. of mol.: 2 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP25, USP21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UHP3, ubiquitinyl hydrolase 1
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.74 Å³/Da / Density % sol: 55.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Hepes pH 7.5 12% w/v PEG4000 0.2 M MgCl2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 26, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8729 Å / Relative weight: 1
Reflection	Resolution: 3.07→48.54 Å / Num. obs: 26854 / % possible obs: 100 % / Redundancy: 26.9 % / B_iso Wilson estimate: 91.88 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.067 / Net I/σ(I): 11.9
Reflection shell	Resolution: 3.07→3.28 Å / Redundancy: 26.9 % / Num. unique obs: 4806 / CC_1/2: 0.509 / R_pim(I) all: 0.754 / % possible all: 100

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Processing

Software

Name	Version	Classification
BUSTER	2.10.2	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6H4I

6h4i

Resolution: 3.07→48.54 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.923 / R_factor R_free error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R_free Blow DPI: 0.365

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23	1365	5.09 %	RANDOM
R_work	0.181	-	-	-
obs	0.183	26827	100 %	-

Displacement parameters

B_iso mean: 104.52 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.8359 Å²	0 Å²	0 Å²
2-	-	5.5638 Å²	0 Å²
3-	-	-	-0.728 Å²

Refine analyze

Luzzati coordinate error obs: 0.38 Å

Refinement step

Cycle: 1 / Resolution: 3.07→48.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7550	0	3	29	7582

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	7747	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.06	10526	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		3514	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		199	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		1135	HARMONIC	5
X-RAY DIFFRACTION	t_it		7747	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	2.67
X-RAY DIFFRACTION	t_other_torsion	3.27
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		988	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies		1	HARMONIC	1
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		8579	SEMIHARMONIC	4

LS refinement shell

Resolution: 3.07→3.19 Å / R_factor R_free error: 0 / Total num. of bins used: 13

	R_factor	Num. reflection	% reflection
R_free	0.284	154	5.14 %
R_work	0.233	2841	-
all	0.235	2995	-
obs	-	-	99.97 %

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	1.7217	0.1602	0.4209	3.8406	1.5412	2.5365	-0.0838	0.479	-0.3791	-0.342	0.5797	-0.2505	0.9545	0.9107	-0.4959	0.176	0.3671	-0.1279	0.1226	-0.2533	-0.1734	-11.7675	-22.3367	-29.3488
2	2.0481	0.5759	1.396	1.9792	2.373	4.8039	0.1546	0.1341	-0.5009	0.6182	0.2428	-0.0779	1.3036	0.8638	-0.3974	0.0452	0.2278	-0.0568	-0.3526	-0.0037	-0.328	-15.5802	-17.2045	-15.1855
3	2.3236	1.2112	2.4219	1.0545	0.5263	3.9601	-0.3525	-0.009	0.1329	-0.1959	-0.022	0.1733	-0.6557	0.2756	0.3746	0.0435	-0.0212	-0.0785	-0.0913	0.0023	-0.1561	-19.8209	6.2844	-16.9984
4	5.0284	-5.1656	5.0134	4.3258	-3.8981	6.4364	-0.2197	-0.7148	0.4168	0.5656	0.283	-0.0743	-0.6452	-0.3848	-0.0632	0.1095	-0.2175	-0.1727	-0.0203	0.0554	-0.0403	-18.1527	23.8589	-19.3974
5	0.1254	1.2542	6.1078	3.8712	3.8679	2.2973	-0.0517	0.3926	-0.113	-0.1797	-0.1984	-0.0402	-0.389	0.2627	0.2501	0.0717	0.0652	-0.056	-0.1592	0.0763	0.0194	-39.531	35.2898	-41.8609
6	2.9161	0.1331	-3.173	0.0031	-0.9011	1.5315	-0.1879	0.6529	0.2988	-0.419	-0.4699	-0.0228	-0.303	-0.5646	0.6578	0.6025	0.2163	-0.1645	-0.0809	0.1475	0.1467	-42.1858	39.9871	-63.7541
7	3.5057	-1.4086	2.3628	0.2121	0.45	4.2645	-0.0486	0.1287	0.4535	-0.3971	-0.1446	-0.3021	-0.6257	0.916	0.1932	0.2843	-0.327	-0.1147	-0.1789	0.2673	0.1546	-26.3444	38.4918	-38.0346
8	2.5241	0.0533	2.0699	4.7627	0.8832	4.6442	-0.0481	0.8741	-0.1177	-0.9212	0.3036	-0.0621	0.1094	1.0411	-0.2555	0.0159	0.0279	0.0382	0.1561	-0.0503	-0.3855	-13.4817	-3.6919	-30.775
9	3.5283	2.886	-2.2997	6.7312	-0.8855	1.1204	-0.0688	-0.0649	-0.6681	-0.6422	-0.0478	-0.341	0.1998	0.264	0.1165	0.5672	0.6138	0.0683	0.3061	-0.5685	0.142	-4.8867	-32.3389	-36.4903
10	3.9453	0.8492	-0.5573	6.75	-5.6494	0.9315	-0.0376	-0.2525	0.6819	-0.0643	0.1366	0.7756	-0.4706	-0.5537	-0.099	0.0573	0.2415	0.3177	-0.4787	-0.2327	0.4895	14.7989	50.4993	-25.4385
11	1.3161	2.2491	-1.6876	3.1567	-0.8015	4.1589	0.225	-1.1533	1.5107	1.3732	-0.012	0.084	-1.2205	0.0712	-0.2129	0.3567	0.0888	0.381	-0.1859	-0.3991	0.5285	18.6648	46.175	-11.734
12	5.4062	0.3101	-3.188	5.3836	-2.8238	2.4083	-0.0184	-0.8885	-0.0004	0.4007	-0.2178	-0.428	0.2346	0.6575	0.2362	0.0259	-0.0357	0.1364	-0.1085	-0.055	-0.0193	25.6704	21.501	-12.4846
13	1.2216	0.1232	0.5292	1.2741	-0.4347	0	0.0639	-0.3883	0.1292	0.4361	-0.0097	0.2918	-0.0476	-0.0812	-0.0542	0.0115	-0.0842	0.0724	-0.0683	-0.0413	-0.143	27.1802	12.8862	-21.4588
14	0.9422	2.2719	3.1739	0	0.6291	0.5835	-0.0488	0.7589	0.3021	0.0487	0.0915	-0.2339	0.3122	0.5665	-0.0427	0.0841	0.161	0.05	0.2002	-0.0935	-0.0737	36.8497	-10.231	-65.1048
15	3.6058	-2.952	-3.9547	6.2144	4.0511	4.9303	0.0662	-0.1416	-0.4402	0.2166	-0.1143	0.5336	0.6896	-0.7412	0.0481	-0.0312	-0.1336	-0.1944	-0.076	0.0033	-0.0057	27.8161	-9.777	-35.3072
16	3.8951	3.6482	-2.1046	4.8606	-3.5729	5.4158	-0.0071	0.1177	0.9667	0.0984	0.6658	0.8367	-0.5096	-0.9658	-0.6587	0.0359	0.1434	0.0868	-0.1084	-0.0807	0.29	15.6961	32.2479	-27.3485
17	0.0206	-1.8789	-1.6816	5.8936	-0.7387	4.8446	0.0592	-0.3935	0.5913	-0.145	0.2175	0.8224	-0.3198	-0.3844	-0.2767	-0.1962	0.0393	0.0661	-0.1699	-0.1628	0.1483	13.9714	33.5726	-23.1745
18	0.2618	2.0196	7.9306	5.6001	3.5765	1.0612	-0.1187	0.1599	0.3645	0.3989	-0.0098	0.0984	-0.2809	-0.1075	0.1284	-0.1269	0.4956	-0.0753	-0.2234	0.0123	0.8044	4.9068	60.9225	-32.567

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{A\|155 - 206}
2	X-RAY DIFFRACTION	2	{A\|217 - 320}
3	X-RAY DIFFRACTION	3	{A\|321 - 405}
4	X-RAY DIFFRACTION	4	{A\|406 - 437}
5	X-RAY DIFFRACTION	5	{A\|438 - 460}
6	X-RAY DIFFRACTION	6	{A\|461 - 541}
7	X-RAY DIFFRACTION	7	{A\|542 - 578}
8	X-RAY DIFFRACTION	8	{A\|579 - 663}
9	X-RAY DIFFRACTION	9	{A\|664 - 706}
10	X-RAY DIFFRACTION	10	{B\|158 - 217}
11	X-RAY DIFFRACTION	11	{B\|218 - 320}
12	X-RAY DIFFRACTION	12	{B\|321 - 357}
13	X-RAY DIFFRACTION	13	{B\|358 - 460}
14	X-RAY DIFFRACTION	14	{B\|461 - 541}
15	X-RAY DIFFRACTION	15	{B\|542 - 578}
16	X-RAY DIFFRACTION	16	{B\|579 - 640}
17	X-RAY DIFFRACTION	17	{B\|641 - 666}
18	X-RAY DIFFRACTION	18	{B\|667 - 704}

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