PDB-6dx5: Crystal structure of the viral OTU domain protease from Farallon virus

ID or keywords:

Entry

Database: PDB / ID: 6dx5

Title

Crystal structure of the viral OTU domain protease from Farallon virus

Components

RNA-dependent RNA polymerase

Keywords

HYDROLASE / PROTEIN BINDING / viral OTU / DUB / Viral Protein

Function / homology

Function and homology information

RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription
Similarity search - Function

Biological species

Farallon virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.224 Å

Authors

Beldon, B.S. / Dzimianski, J.V. / Daczkowski, C.M. / Goodwin, O.Y. / Pegan, S.D.

Funding support

United States, 1items

Citation

Journal: PLoS Pathog. / Year: 2019
Title: Probing the impact of nairovirus genomic diversity on viral ovarian tumor domain protease (vOTU) structure and deubiquitinase activity.
Authors: Dzimianski, J.V. / Beldon, B.S. / Daczkowski, C.M. / Goodwin, O.Y. / Scholte, F.E.M. / Bergeron, E. / Pegan, S.D.

History

Deposition	Jun 28, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 19, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 2023	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	6dx5.cif.gz	161.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6dx5.ent.gz	128.3 KB	Display	PDB format
PDBx/mmJSON format	6dx5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6dx5_validation.pdf.gz	455.7 KB	Display	wwPDB validaton report
Full document	6dx5_full_validation.pdf.gz	459.6 KB	Display
Data in XML	6dx5_validation.xml.gz	17.1 KB	Display
Data in CIF	6dx5_validation.cif.gz	23.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dx/6dx5 ftp://data.pdbj.org/pub/pdb/validation_reports/dx/6dx5	HTTPS FTP

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Related structure data

Related structure data	6dwxC 6dx1C 6dx2C 6dx3C 4hxdS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6fdw-2 4mjv-d 3m8n-1 2yxw-1 3ly2-1 5h2q-2 6gxq-2 6kk0-1 3qvd-4 6fv9-2 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	#92 - Aug 2007 Anabolic Steroids similarity (1) #127 - Jul 2010 Crystallins similarity (1) #174 - Jun 2014 GFP-like Proteins similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

B: RNA-dependent RNA polymerase

A: RNA-dependent RNA polymerase

hetero molecules

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

1

B: RNA-dependent RNA polymerase

hetero molecules

A: RNA-dependent RNA polymerase

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.276, 70.276, 176.258
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	RNA-dependent RNA polymerase Mass: 23043.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Farallon virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A191KW96
#2: Chemical	ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₂S₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.36 Å³/Da / Density % sol: 47.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.3 M magnesium chloride, 0.1 M MES pH 6.5, 8% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.22→50 Å / Num. obs: 22465 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC_1/2: 0.99 / Net I/σ(I): 18.9
Reflection shell	Resolution: 2.22→2.26 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2182 / CC_1/2: 0.89

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4HXD

4hxd

Resolution: 2.224→37.941 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.28

	R_factor	Num. reflection	% reflection
R_free	0.2025	1136	5.06 %
R_work	0.163	-	-
obs	0.1651	22455	99.59 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.224→37.941 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2730	0	24	169	2923

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	2815
X-RAY DIFFRACTION	f_angle_d	1.228	3804
X-RAY DIFFRACTION	f_dihedral_angle_d	14.98	1614
X-RAY DIFFRACTION	f_chiral_restr	0.069	406
X-RAY DIFFRACTION	f_plane_restr	0.007	488

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 (%)
2.2243-2.3255	0.2379	146	0.198	2591	X-RAY DIFFRACTION	99
2.3255-2.4481	0.2659	116	0.1891	2617	X-RAY DIFFRACTION	100
2.4481-2.6015	0.2389	155	0.1931	2633	X-RAY DIFFRACTION	100
2.6015-2.8023	0.2694	130	0.1902	2641	X-RAY DIFFRACTION	100
2.8023-3.0842	0.231	135	0.1859	2643	X-RAY DIFFRACTION	99
3.0842-3.5302	0.1936	150	0.1572	2645	X-RAY DIFFRACTION	99
3.5302-4.4465	0.1573	146	0.1357	2700	X-RAY DIFFRACTION	100
4.4465-37.9469	0.1867	158	0.1491	2849	X-RAY DIFFRACTION	99

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	2.5689	-1.1452	-4.0414	1.7319	2.4791	6.7499	1.0863	-0.3143	1.3711	-0.0132	0.6459	-1.6141	-0.5335	1.9085	-1.0929	0.3969	-0.043	0.0026	0.869	0.031	0.7394	23.4284	36.3052	-37.0551
2	4.002	1.5148	5.8492	1.9957	0.9598	9.6906	0.3046	1.1926	-0.3206	0.1092	0.0219	-0.4518	0.4015	1.0182	-0.3421	0.2893	0.1741	0.1076	0.684	0.0318	0.2844	20.1671	29.579	-43.8101
3	8.0028	4.3056	1.5516	5.3149	-1.766	2.5549	0.051	-2.1625	0.0066	0.3347	-0.2173	-0.9361	0.2353	0.7961	0.1527	0.2565	0.0403	-0.046	0.7545	-0.0242	0.5164	21.9806	30.6793	-27.972
4	2.7264	1.7714	-2.178	2.8093	-4.6042	7.9182	0.8936	-2.1545	0.5291	1.2287	-0.4617	-0.5598	-0.8486	1.3635	-0.3977	0.4117	-0.1427	0.0534	0.6045	-0.1528	0.4283	12.0669	33.6831	-23.0926
5	3.1753	-0.5764	1.7673	3.4177	-0.8295	7.1397	0.2752	-0.0964	-0.1605	-0.1997	-0.0903	0.0672	0.392	-0.1784	-0.175	0.194	0.0562	-0.0406	0.2279	0.0019	0.225	1.1834	25.7548	-32.5839
6	4.0772	-1.2654	3.4133	3.3541	2.8633	8.055	-0.243	-0.7033	0.4838	0.6367	-0.1846	0.2243	-0.0913	-1.3412	-0.0366	0.2487	0.0426	-0.034	0.3399	-0.0003	0.3208	-4.5547	30.8162	-33.5656
7	0.6409	0.2168	-0.9782	1.5253	1.0995	3.9544	0.4166	0.261	-0.2075	-0.4388	-0.3135	0.0565	0.4436	0.5306	0.0898	0.4369	0.2155	-0.0964	0.3331	-0.0264	0.2827	0.6502	24.648	-47.9459
8	3.8628	-0.9765	-0.4719	6.7427	1.3414	8.4251	0.6618	0.4177	0.0211	-0.0635	0.7285	-1.1351	0.0598	0.7018	-0.1876	0.4685	0.4687	-0.0384	0.6713	-0.2206	0.4197	12.5281	22.3488	-51.8637
9	1.7189	1.8566	1.0687	2.1037	2.0374	8.0169	0.26	0.0941	-0.5612	0.0611	0.3513	-0.5091	0.9676	0.9879	0.085	0.8324	0.919	-0.7442	0.8395	-0.2422	0.4476	13.2615	12.8083	-51.8869
10	4.0451	-3.2297	-2.4258	5.7258	5.066	7.5917	-0.4013	0.5083	-0.5246	0.2712	-0.0532	0.4319	0.2695	0.2253	0.3128	1.1916	0.5496	-0.2086	0.8492	-0.0343	1.0963	12.0862	7.0631	-55.5065
11	7.3673	2.3619	-2.4552	3.8839	2.3612	3.9835	-0.194	-0.7593	0.5023	-1.2491	-0.3554	0.8474	0.361	-0.0948	0.1842	1.1248	0.4586	-0.3364	1.191	-0.1612	0.8356	11.3789	9.477	-62.8811
12	4.5904	2.2406	-5.7773	4.8816	-3.1716	8.1086	0.3619	1.5297	-0.8613	-1.0497	-0.0308	0.1711	1.2159	-0.6924	0.093	0.9533	0.3408	-0.277	0.6284	-0.1596	0.4652	5.249	13.5079	-56.727
13	9.7478	0.1935	-7.6607	0.7669	-0.5522	6.2333	-0.3772	0.0843	-0.862	0.1399	0.1411	0.2006	1.8472	0.1035	-0.6673	0.9002	0.2674	-0.2942	0.4113	-0.1279	0.3185	1.0256	13.6293	-47.7463
14	5.3967	2.3141	1.3113	5.3339	-0.9391	5.5927	0.2685	-0.1631	-0.1422	0.2165	0.0019	-0.1211	0.9757	-0.5012	-0.3398	0.6061	0.1409	-0.1563	0.3684	-0.0843	0.337	3.2324	16.4072	-39.0623
15	6.102	-0.0466	3.0383	2.3606	-0.4531	6.405	0.442	0.6017	-0.018	-0.5833	-0.1811	-0.0996	0.3249	0.3011	-0.3151	0.273	0.1142	0.0117	0.2845	-0.0016	0.229	8.5164	29.5329	-43.6567
16	5.804	0.5148	-0.8894	6.6947	-5.5288	4.6123	0.0024	-0.4432	0.0658	0.7011	-0.213	-0.3625	-0.1001	0.4233	0.2205	0.2723	0.0806	-0.0094	0.366	-0.0623	0.2904	17.3531	24.7191	-25.7502
17	5.219	-2.0198	5.8457	0.7824	-2.2946	6.8243	0.335	0.6089	0.0615	-0.0598	-0.3608	0.1964	0.5593	0.782	-0.2187	0.3019	0.1433	0.0152	0.4856	0.0166	0.2354	16.9668	28.9024	-38.573
18	4.1683	-2.5495	-4.898	5.9946	6.8097	9.0351	0.6028	0.8703	0.993	-1.0272	-0.9727	-0.1876	-1.0761	-1.4585	-0.0358	0.3252	0.0279	0.0527	0.5564	0.1099	0.4334	13.5149	40.1496	-38.0939
19	2.9197	0.2466	-0.114	2.312	0.3096	3.2635	0.134	0.0972	-0.1182	0.071	0.0165	-0.1391	0.258	0.2262	-0.1257	0.1595	0.0319	-0.0323	0.2694	-0.0105	0.2407	9.1224	26.2218	-31.2104
20	8.2224	1.45	-2.6401	2.8439	-3.3133	3.9782	-0.941	0.51	3.1233	-0.1519	-0.2285	0.9934	-3.0544	0.9153	0.5063	1.0055	-0.091	-0.0069	0.4805	-0.0645	0.8315	9.2751	40.8469	-26.4232
21	4.1494	2.5706	-3.0784	1.8592	-1.7907	2.3351	0.2446	1.5782	2.128	-0.8118	1.2363	2.1147	-1.5031	-2.9393	-1.3685	0.6548	0.1493	-0.0292	0.9404	0.168	0.7924	-23.4138	34.3837	-10.9274
22	4.1008	1.4423	4.6218	2.0113	0.218	6.6363	0.1045	0.3394	-0.4802	0.184	0.3057	0.5099	0.1179	-1.2103	-0.1518	0.4682	-0.0855	0.0715	0.6457	0.0332	0.4447	-20.2862	25.9637	-0.4759
23	3.28	-0.2047	0.1512	2.0608	-0.4592	1.7389	-0.2635	0.3689	0.3707	-0.3994	0.2764	0.8339	0.4521	-1.6982	-0.148	0.4388	-0.1931	-0.0551	0.6715	0.146	0.4341	-21.6286	27.0889	-11.68
24	6.1805	-5.0831	-3.3517	4.1974	2.871	2.3018	0.5383	1.6901	0.5473	-0.8974	-0.243	0.349	-0.3426	-0.7514	-0.2396	0.2502	0.0394	-0.0104	0.5174	0.1252	0.355	-12.1459	31.6758	-22.6486
25	2.632	0.6704	1.9184	2.8853	-0.0626	6.0986	0.1391	0.2279	-0.1665	-0.043	-0.0061	0.0985	0.0469	0.1707	-0.0834	0.1586	-0.0431	-0.0129	0.2412	0.0033	0.2094	0.0445	25.5736	-13.6265
26	7.6498	5.1935	5.0583	4.9673	5.3292	6.6192	-0.2663	0.6445	0.5462	0.0237	0.3197	-0.1	0.1244	0.554	-0.1222	0.2024	-0.1132	-0.0256	0.3032	0.0493	0.3293	5.0992	31.2103	-12.6033
27	6.3321	0.4874	-5.3598	3.5482	-0.5778	8.7922	0.3506	-0.3365	-0.0774	0.4198	-0.1123	-0.374	-0.2599	0.5563	-0.2214	0.2112	-0.0428	-0.0758	0.1734	-0.0119	0.2401	2.9764	25.0011	-1.0866
28	7.8827	5.3802	2.7239	4.6829	2.8576	2.5916	0.2668	0.0051	0.961	1.3427	-0.3325	-0.0459	0.3677	-0.2522	0.0724	0.3602	-0.1652	-0.0455	0.4031	0.0453	0.338	-5.8037	23.2113	9.4929
29	3.3281	-0.2841	1.0718	5.9038	-2.2003	1.9742	0.3989	-0.483	-0.232	0.396	-0.0722	0.3892	0.6149	-0.3133	-0.2872	0.3931	-0.1686	-0.068	0.3374	0.0609	0.3025	-9.3616	15.7621	5.2212
30	3.6893	-0.0082	-0.5727	5.5062	-3.8594	7.6111	0.3259	-0.6468	-2.306	0.1502	-0.3879	-0.0466	2.2501	-0.3846	0.3176	0.8394	-0.1957	-0.1958	0.4761	0.1386	0.8259	-8.3674	4.7873	10.3228
31	7.2335	-0.6914	0.7959	1.9486	-1.5633	2.0366	0.0306	-1.0026	-0.3768	1.9235	-0.0875	0.5084	0.1299	0.502	0.0216	0.9932	-0.261	-0.0659	0.6612	0.1191	0.5776	-6.4935	10.8464	16.5389
32	6.9486	3.6768	-5.1946	5.1515	-4.3676	4.6988	0.2923	-0.97	-1.0396	0.4863	-0.6057	-0.5908	0.8829	1.1866	0.3127	0.5307	-0.0782	-0.1534	0.2914	0.1242	0.3675	-0.5015	12.9649	8.2381
33	9.9901	-0.4961	-6.8993	4.5694	-0.214	5.9117	-0.3121	-0.0295	-1.4294	-0.5993	-0.6977	-0.834	1.7573	0.9981	0.821	0.5155	0.0937	-0.0238	0.349	0.0673	0.4391	4.6516	13.1737	-2.7125
34	3.446	-1.0971	0.1692	2.7138	-0.5617	2.171	0.0888	-0.2381	-0.0943	0.308	0.0266	0.1878	0.217	0.0121	-0.0443	0.2335	-0.0706	-0.0231	0.2438	0.0185	0.2353	-6.1228	25.113	-3.3337
35	8.9197	-5.6724	-8.5024	8.0418	5.7136	8.4254	-0.1919	0.5772	-0.3576	-0.4676	-0.5508	0.8996	0.0483	-0.3571	0.7611	0.242	-0.1062	0.0026	0.2888	0.005	0.2772	-14.6144	22.4707	-18.7207
36	5.0852	1.0864	-0.1224	9.2105	6.6828	5.0758	-0.2264	0.2445	-0.2155	-0.1036	-0.0762	0.6231	0.1506	-0.5787	0.164	0.2257	-0.0977	-0.048	0.2749	0.0588	0.3429	-17.3091	24.2131	-15.392
37	7.2295	0.1042	-0.0453	4.0329	-4.6984	9.8682	0.1964	-0.3658	0.3531	0.3561	-0.1133	0.0485	-0.7035	-0.1232	-0.0001	0.2177	-0.0083	0.0796	0.3534	-0.0848	0.4455	-14.6164	33.6894	-5.407
38	3.6423	-3.609	3.8607	3.629	-3.9007	4.2029	0.0092	-0.2061	0.1665	0.2559	0.0154	0.7971	-1.1883	-0.0121	-0.0553	0.3203	-0.0066	0.0031	0.2651	0.0026	0.3332	-10.4194	36.3052	-10.2037
39	4.5649	-0.1957	-0.3096	9.9552	-3.9788	4.3287	-0.0842	-0.1569	-0.41	-0.4226	-0.031	-0.2109	0.2959	-0.2114	0.1193	0.1855	-0.0714	-0.0164	0.2544	-0.0146	0.2182	-7.4446	22.4237	-16.059
40	2.0014	4.3555	3.1723	4.8672	6.4967	9.7704	-0.541	0.629	4.2672	-0.3646	-0.7678	0.1487	-2.9598	-0.5286	0.681	0.784	0.0207	-0.1373	0.4414	0.1553	0.8499	-10.2228	39.2061	-19.5583

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:8)
2	X-RAY DIFFRACTION	2	(chain A and resid 9:16)
3	X-RAY DIFFRACTION	3	(chain A and resid 17:22)
4	X-RAY DIFFRACTION	4	(chain A and resid 23:28)
5	X-RAY DIFFRACTION	5	(chain A and resid 29:46)
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