PDB-9qy8: Crystal structure of apoform human USP18

ID or keywords:

Entry

Database: PDB / ID: 9qy8

Title

Crystal structure of apoform human USP18

Components

Ubl carboxyl-terminal hydrolase 18,Response regulator FrzS

Keywords

HYDROLASE / UBIQUITIN-SPECIFIC PROTEASE / ISG15 / INTERFERON

Function / homology

Function and homology information

response to stilbenoid / negative regulation of type I interferon-mediated signaling pathway / phosphorelay signal transduction system / Regulation of IFNA/IFNB signaling / protein deubiquitination / antiviral innate immune response / response to bacterium / Regulation of NF-kappa B signaling / regulation of protein stability / TAK1-dependent IKK and NF-kappa-B activation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Myxococcus xanthus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.919 Å

Authors

Turnbull, A.P. / Halliwell, T. / Frankling, C.L.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Crystal structure of apoform human USP18
Authors: Turnbull, A.P. / Halliwell, T. / Frankling, C.

History

Deposition	Apr 17, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 29, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9qy8.cif.gz	458.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9qy8.ent.gz	291.8 KB	Display	PDB format
PDBx/mmJSON format	9qy8.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/qy/9qy8 ftp://data.pdbj.org/pub/pdb/validation_reports/qy/9qy8	HTTPS FTP

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Related structure data

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	#128 - Aug 2010 Interferons similarity (2) #190 - Oct 2015 Two-component Systems similarity (5) #122 - Feb 2010 Enhanceosome similarity (1) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Ubl carboxyl-terminal hydrolase 18,Response regulator FrzS

B: Ubl carboxyl-terminal hydrolase 18,Response regulator FrzS

hetero molecules

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

1

A: Ubl carboxyl-terminal hydrolase 18,Response regulator FrzS

hetero molecules

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

2

B: Ubl carboxyl-terminal hydrolase 18,Response regulator FrzS

hetero molecules

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

Unit cell

Length a, b, c (Å)	47.868, 71.775, 73.063
Angle α, β, γ (deg.)	79.320, 76.283, 89.882
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	A
3	2	A
4	2	A

NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	TYR	TYR	GLU	GLU	50 - 371	4 - 439
2	1	1	TYR	TYR	GLU	GLU	50 - 371	4 - 439
3	2	2	GLY	GLY	SER	SER	401 - 528	240 - 367
4	2	2	GLY	GLY	SER	SER	401 - 528	240 - 367

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4

#1: Protein	Ubl carboxyl-terminal hydrolase 18,Response regulator FrzS / 43 kDa ISG15-specific protease / hUBP43 / ISG15-specific-processing protease / Ubl thioesterase 18 Mass: 49748.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: USP18 and the FrzS insert Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Myxococcus xanthus (strain DK1622) (bacteria) Gene: USP18, ISG43, frzS, MXAN_4149 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9UMW8, UniProt: Q1D4U9, ubiquitinyl hydrolase 1
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 49 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane, pH 7.5, 20 % (w/v) PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 4, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.919→39.593 Å / Num. obs: 69489 / % possible obs: 97.9 % / Redundancy: 3.6 % / CC_1/2: 0.996 / R_merge(I) obs: 0.071 / Net I/σ(I): 17.9
Reflection shell	Resolution: 1.92→1.95 Å / R_merge(I) obs: 2.455 / Num. unique obs: 3316 / CC_1/2: 0.342

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.919→39.593 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.947 / SU B: 15.244 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / ESU R: 0.169 / ESU R Free: 0.164
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2601	2020	2.922 %
R_work	0.2048	67118	-
all	0.206	-	-
obs	-	69138	97.436 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 55.037 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.879 Å²	-0.944 Å²	-0.39 Å²
2-	-	-2.278 Å²	-0.261 Å²
3-	-	-	0.084 Å²

Refinement step

Cycle: LAST / Resolution: 1.919→39.593 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4829	0	1904	223	6956

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	6880
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6470
X-RAY DIFFRACTION	r_angle_refined_deg	1.724	1.817	9338
X-RAY DIFFRACTION	r_angle_other_deg	0.61	1.747	14867
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.28	5	877
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.959	5	34
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.836	10	1108
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.948	10	288
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	1082
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	8050
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1530
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	1273
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	5881
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	3355
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	3851
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	256
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.252	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.256	0.2	32
X-RAY DIFFRACTION	r_nbd_other	0.237	0.2	105
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.189	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	3.746	3.836	3502
X-RAY DIFFRACTION	r_mcbond_other	3.746	3.835	3502
X-RAY DIFFRACTION	r_mcangle_it	5.157	6.879	4375
X-RAY DIFFRACTION	r_mcangle_other	5.156	6.878	4376
X-RAY DIFFRACTION	r_scbond_it	4.46	4.072	3378
X-RAY DIFFRACTION	r_scbond_other	4.459	4.072	3379
X-RAY DIFFRACTION	r_scangle_it	6.256	7.366	4961
X-RAY DIFFRACTION	r_scangle_other	6.255	7.366	4962
X-RAY DIFFRACTION	r_lrange_it	7.894	39.532	7362
X-RAY DIFFRACTION	r_lrange_other	7.887	39.36	7340
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.101	0.05	9192
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.057	0.05	3893

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.10085	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10085	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.0571	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.0571	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.919-1.969	0.458	135	0.416	4628	0.417	5226	0.826	0.839	91.1404	0.419
1.969-2.022	0.436	145	0.401	4707	0.402	5066	0.868	0.858	95.7758	0.407
2.022-2.081	0.375	142	0.36	4712	0.36	5023	0.898	0.894	96.6355	0.343
2.081-2.145	0.429	138	0.335	4541	0.338	4821	0.882	0.912	97.0546	0.316
2.145-2.215	0.32	121	0.293	4423	0.294	4657	0.93	0.936	97.5735	0.265
2.215-2.292	0.387	146	0.294	4295	0.297	4554	0.887	0.935	97.5187	0.266
2.292-2.378	0.332	126	0.265	4115	0.267	4341	0.941	0.954	97.6964	0.228
2.378-2.475	0.267	102	0.249	4018	0.25	4210	0.945	0.961	97.8622	0.209
2.475-2.585	0.298	118	0.243	3821	0.245	4013	0.95	0.965	98.156	0.203
2.585-2.71	0.268	114	0.216	3669	0.218	3849	0.96	0.971	98.2853	0.177
2.71-2.856	0.294	94	0.214	3530	0.216	3684	0.948	0.974	98.3713	0.178
2.856-3.029	0.255	106	0.209	3317	0.211	3472	0.964	0.975	98.5887	0.178
3.029-3.236	0.255	107	0.21	3083	0.212	3232	0.959	0.975	98.7005	0.185
3.236-3.494	0.235	93	0.202	2924	0.203	3054	0.966	0.978	98.7885	0.188
3.494-3.824	0.269	65	0.193	2691	0.195	2783	0.967	0.98	99.0298	0.183
3.824-4.271	0.197	59	0.149	2461	0.15	2540	0.977	0.987	99.2126	0.143
4.271-4.922	0.195	72	0.129	2125	0.131	2211	0.982	0.991	99.3668	0.127
4.922-6.005	0.237	67	0.179	1836	0.181	1915	0.972	0.985	99.3734	0.176
6.005-8.396	0.208	42	0.178	1407	0.179	1454	0.974	0.983	99.6561	0.181
8.396-39.593	0.23	28	0.156	815	0.159	846	0.971	0.985	99.6454	0.184

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	2.7605	-0.7499	-0.99	2.5644	0.853	2.8617	-0.111	-0.0401	0.2043	0.165	-0.087	0.0611	-0.0266	-0.2062	0.1981	0.0529	-0.0167	-0.0694	0.0331	0.0053	0.1366	-13.0155	-25.3856	32.5744
2	1.7829	-1.4961	0.2131	5.3135	-0.665	1.5766	0.0386	-0.0632	-0.1867	-0.2534	0.1081	0.0256	0.0237	-0.1033	-0.1467	0.0837	-0.0268	0.0091	0.0293	-0.0186	0.1037	0.3146	-64.0753	26.3084
3	2.4238	1.2875	0.513	4.4566	0.5326	2.3627	0.0271	0.1519	-0.1054	-0.2218	-0.0914	0.1646	0.1184	-0.3785	0.0643	0.0242	-0.0095	-0.0227	0.0891	-0.0364	0.1036	-19.3939	-66.7054	65.27
4	2.0225	1.7486	-1.0676	5.293	-0.9883	3.0856	0.0474	0.03	0.232	0.1498	-0.0862	0.1085	-0.3632	0.173	0.0387	0.0818	-0.0124	-0.0698	0.0246	-0.0056	0.1193	-6.0909	-28.1466	71.3258
5	7.5565	1.305	3.0454	8.0571	1.3043	6.6773	0.2899	-0.0069	0.5099	0.5749	0.1376	-0.0938	-0.1776	0.1469	-0.4275	0.3347	-0.039	-0.0159	0.4121	0.0197	0.2962	8.4717	-45.77	44.9039
6	1.3428	1.2432	-0.7137	1.2417	-0.9403	5.8462	0.0633	0.0836	-0.1069	-0.0043	0.0924	0.0528	0.0377	0.0269	-0.1557	0.2543	0.0151	-0.0045	0.2926	-0.0034	0.343	-3.6957	-47.8952	54.4216

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	49 - 183
2	X-RAY DIFFRACTION	1	ALL	A	178 - 219
3	X-RAY DIFFRACTION	1	ALL	A	241 - 285
4	X-RAY DIFFRACTION	1	ALL	A	300 - 372
5	X-RAY DIFFRACTION	2	ALL	A	1000 - 1126
6	X-RAY DIFFRACTION	5	ALL	A	177 - 184
7	X-RAY DIFFRACTION	5	ALL	A	220 - 240

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