PDB-5af2: Crystal structure of the C-terminal 2',5'-phosphodiesterase domai...

ID or keywords:

Entry

Database: PDB / ID: 5af2

Title

Crystal structure of the C-terminal 2',5'-phosphodiesterase domain of group A rotavirus protein VP3

Components

VP3

Keywords

HYDROLASE / PHOSPHODIESTERASE / 2-5A / 2H PHOSPHOESTERASE / RNASE L / OLIGOADENYLATE SYNTHASE / INNATE IMMUNITY / IMMUNE EVASION

Function / homology

Function and homology information

RNA 5'-cap (guanine-N7)-methylation / : / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / mRNA guanylyltransferase activity / viral nucleocapsid / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / hydrolase activity ...
Similarity search - Function

Biological species

ROTAVIRUS A

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.39 Å

Authors

Brandmann, T. / Jinek, M.

Citation

Journal: Proteins / Year: 2015
Title: Crystal Structure of the C-Terminal 2',5'-Phosphodiesterase Domain of Group a Rotavirus Protein Vp3.
Authors: Brandmann, T. / Jinek, M.

History

Deposition	Jan 16, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 18, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 25, 2015	Group: Database references
Revision 1.2	Apr 8, 2015	Group: Atomic model
Revision 1.3	Apr 29, 2015	Group: Database references
Revision 1.4	May 8, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5af2.cif.gz	361.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5af2.ent.gz	303.3 KB	Display	PDB format
PDBx/mmJSON format	5af2.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5af2_validation.pdf.gz	916 KB	Display	wwPDB validaton report
Full document	5af2_full_validation.pdf.gz	919.4 KB	Display
Data in XML	5af2_validation.xml.gz	28.4 KB	Display
Data in CIF	5af2_validation.cif.gz	42.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/af/5af2 ftp://data.pdbj.org/pub/pdb/validation_reports/af/5af2	HTTPS FTP

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Related structure data

Similar structure data	2jzh-d 3kf9-2 5etx-2 3qp1-d 3urg-d 3zxc-d 1nrz-2 2k0f-d 3qp4-d 5j8h-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (2) #103 - Jul 2008 Dengue Virus similarity (1) #197 - May 2016 Zika Virus similarity (1)

Deposited unit

A: VP3

B: VP3

C: VP3

D: VP3

hetero molecules

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

1

A: VP3

hetero molecules

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

2

B: VP3

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

3

C: VP3

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

4

D: VP3

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

Unit cell

Length a, b, c (Å)	61.290, 74.960, 63.220
Angle α, β, γ (deg.)	90.00, 112.80, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	VP3 Mass: 16749.520 Da / Num. of mol.: 4 / Fragment: PHOSPHODIESTERASE DOMAIN, RESIDUES 696-835 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ROTAVIRUS A / Strain: SA11 / Plasmid: 1M / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: A2T3S1, UniProt: A2T3S5*PLUS
#2: Chemical	ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆₉H₁₄₀O₃₅ / Comment: precipitant*YM
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	N-TERMINAL SNA SEQUENCE IS DERIVED FROM THE EXPRESSED FUSION PROTEIN

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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 Å³/Da / Density % sol: 38.5 % / Description: NONE
Crystal grow	pH: 7 Details: 0.1 M TRIS-ACETATE PH 7.0, 0.2 M KSCN AND 22 % PEG MONOMETHYL ETHER 2000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
Detector	Type: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 4, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.39→45.12 Å / Num. obs: 105693 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / R_merge(I) obs: 0.07 / Net I/σ(I): 20.1
Reflection shell	Resolution: 1.39→1.43 Å / Redundancy: 11.7 % / R_merge(I) obs: 0.62 / Mean I/σ(I) obs: 3.7 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.39→45.119 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 19.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1928	1986	1.9 %
R_work	0.1713	-	-
obs	0.1717	105679	99.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 21.8 Å²

Refinement step

Cycle: LAST / Resolution: 1.39→45.119 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4660	0	72	597	5329

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4878
X-RAY DIFFRACTION	f_angle_d	1.122	6577
X-RAY DIFFRACTION	f_dihedral_angle_d	12.453	1865
X-RAY DIFFRACTION	f_chiral_restr	0.069	742
X-RAY DIFFRACTION	f_plane_restr	0.005	805

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 (%)
1.39-1.4248	0.2522	133	0.2414	7282	X-RAY DIFFRACTION	98
1.4248-1.4633	0.2374	150	0.2209	7367	X-RAY DIFFRACTION	100
1.4633-1.5064	0.1951	134	0.2112	7359	X-RAY DIFFRACTION	100
1.5064-1.555	0.2121	147	0.1961	7363	X-RAY DIFFRACTION	100
1.555-1.6106	0.2381	140	0.1872	7430	X-RAY DIFFRACTION	100
1.6106-1.6751	0.2008	144	0.185	7370	X-RAY DIFFRACTION	100
1.6751-1.7513	0.212	136	0.1833	7452	X-RAY DIFFRACTION	100
1.7513-1.8436	0.2145	142	0.1793	7357	X-RAY DIFFRACTION	100
1.8436-1.9592	0.2043	147	0.1694	7425	X-RAY DIFFRACTION	100
1.9592-2.1104	0.1613	137	0.1589	7431	X-RAY DIFFRACTION	100
2.1104-2.3228	0.1908	139	0.1584	7411	X-RAY DIFFRACTION	100
2.3228-2.6589	0.1989	147	0.1708	7452	X-RAY DIFFRACTION	100
2.6589-3.3497	0.1898	141	0.1684	7442	X-RAY DIFFRACTION	100
3.3497-45.1426	0.1728	149	0.1585	7552	X-RAY DIFFRACTION	100

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	0.6136	0.0549	-0.0485	0.0903	0.0508	0.058	-0.0132	-0.5007	-0.0273	-0.0643	0.1248	0.1701	0.0347	-0.1702	0.0524	0.1382	-0.0229	-0.0088	0.1808	0.037	0.1185	12.4822	4.192	29.9228
2	0.3994	-0.0609	-0.0538	0.184	0.0595	0.0245	0.0234	-0.3832	0.324	0.2245	-0.0304	-0.0285	-0.0781	-0.0379	-0.0111	0.1315	0.0205	0.0132	0.1546	-0.0797	0.2008	6.5143	19.4502	25.0851
3	0.2672	-0.2479	-0.0358	0.191	0.0629	0.2286	-0.2085	-0.3251	0.0175	0.0671	0.217	0.0263	-0.0183	-0.0414	-0.0674	0.1245	0.0206	-0.0082	0.208	-0.0114	0.0978	21.4866	4.1917	34.0571
4	0.1389	-0.0993	-0.0728	0.0792	-0.0065	0.0986	0.029	0.1343	0.1679	0.0064	0.0306	-0.0754	0.0119	0.1321	0.0052	0.1138	0.0018	0.0124	0.102	-0.0058	0.1507	14.5119	15.5123	17.0874
5	0.0603	-0.0534	-0.0651	0.079	0.0314	0.1033	0.0931	0.1286	0.11	0.0283	-0.0603	-0.0176	0.0482	-0.0248	0.0072	0.099	0.0078	0.0168	0.1056	-0.0112	0.1317	9.8655	12.5799	16.4794
6	0.2828	0.0737	-0.0047	0.0853	-0.0521	0.0338	0.0866	-0.1452	-0.0656	-0.042	-0.0472	-0.0042	0.0176	-0.0483	-0.0634	0.0995	-0.0134	0.0008	0.0968	0.0178	0.1023	20.2869	2.5496	23.5181
7	0.1639	-0.0288	-0.0908	0.1414	0.0289	0.2468	0.0679	0.0593	0.4231	0.0677	0.0432	0.0516	-0.0941	-0.1117	0.0244	0.1508	0.0149	0.0151	0.1144	0.0126	0.2194	8.4282	20.328	15.501
8	0.3117	-0.1585	0.0384	0.1117	-0.0703	0.0971	-0.2056	-0.5419	0.1847	0.0988	0.2529	0.1912	-0.0572	-0.272	0.003	0.1618	0.0265	-0.009	0.29	-0.0413	0.1283	13.6972	10.4384	33.8343
9	0.0937	-0.0229	0.1089	0.4671	-0.0372	0.1928	-0.1949	-0.1602	0.0243	0.0828	0.1641	0.1738	-0.1992	-0.2339	0.0273	0.1763	0.0532	-0.0019	0.3767	-0.0788	0.1005	13.5685	8.7129	36.9987
10	0.2569	0.2431	0.0391	0.4202	0.1196	0.1844	0.0344	0.0996	0.0046	-0.1465	-0.0235	-0.1107	-0.0946	-0.0016	-0.0663	0.1334	0.0188	0.0192	0.084	-0.002	0.0887	5.3379	9.0288	56.5598
11	0.1702	0.1382	-0.071	0.3317	0.0665	0.1615	0.0623	0.0235	0.0692	0.0081	-0.0323	-0.0314	-0.0175	0.0295	0.1044	0.1056	0.0021	0.0148	0.0739	0.0076	0.1093	6.9896	15.8098	70.7746
12	0.2137	-0.0532	-0.1938	0.1616	0.1077	0.162	0.0731	0.0609	-0.038	0.012	-0.0837	-0.0511	0.0091	-0.0363	-0.0786	0.1066	0.01	-0.0018	0.0864	-0.0127	0.0961	1.1278	2.8248	63.8977
13	0.0591	-0.0021	-0.0992	0.1708	-0.1026	0.1852	0.0137	0.0081	0.1417	0.0264	0.0048	-0.143	-0.1629	0.0271	0.008	0.1709	-0.0079	0.0251	0.1188	-0.0223	0.183	10.0254	22.1828	72.2653
14	0.0674	0.031	0.0328	0.0235	0.0139	0.0413	-0.0813	0.1671	0.0413	-0.216	0.0625	-0.196	-0.1884	0.1331	-0.0131	0.1948	0.0241	0.0261	0.1495	0.0055	0.1026	6.6576	11.6987	53.6293
15	0.0647	0.0996	-0.0278	0.143	-0.0135	0.0843	-0.1127	-0.1441	0.0009	-0.1095	0.0544	-0.103	-0.25	0.0896	-0.0127	0.2321	0.0239	0.0064	0.2065	-0.0047	0.1182	6.9936	9.973	50.4472
16	0.9007	0.1295	0.1529	0.371	-0.2378	0.5954	0.126	-0.2119	-0.068	0.036	-0.0692	0.0201	-0.0334	0.0944	0.1139	0.1147	-0.0234	0.0027	0.1523	-0.0015	0.1063	-13.2113	5.5702	28.8145
17	0.3433	-0.0791	0.0811	0.0264	-0.0097	0.0422	0.1332	-0.0384	-0.0858	-0.0318	0.0184	0.0986	0.1051	0.0278	0.0699	0.1091	-0.0016	-0.0289	0.0884	0.021	0.1394	-23.2594	-2.1495	19.3167
18	0.2067	0.0756	0.0726	0.243	-0.1673	0.1755	0.126	-0.2976	0.1131	-0.0374	0.1044	0.199	-0.11	-0.0555	0.0695	0.1501	0.0011	0.0396	0.1889	-0.0384	0.1611	-23.3311	11.8387	31.5134
19	0.0285	0.0035	-0.0333	0.0186	-0.0136	0.0399	0.1437	0.0733	-0.0184	0.1565	-0.0294	-0.1148	0.048	0.0747	0.0037	0.1154	0.0271	-0.0225	0.0945	0.0048	0.1271	-17.5321	0.1648	15.9743
20	0.1969	-0.0199	0.2254	0.3092	-0.054	0.2882	0.1702	0.0956	-0.2971	-0.1224	-0.0513	-0.0325	0.277	0.1718	0.0542	0.1991	0.024	-0.0842	0.0943	0.0153	0.2355	-21.5785	-7.9852	15.1145
21	0.1135	-0.0137	0.0208	0.0254	0.0057	0.046	0.0647	-0.1866	-0.1803	-0.0707	0.0401	-0.1139	0.0206	0.1413	0.0087	0.1088	-0.0077	-0.0026	0.1875	0.0142	0.1348	-9.1342	3.7365	29.0053
22	0.0943	-0.0755	-0.0495	0.1202	0.116	0.1116	0.1043	-0.2111	-0.024	0.0334	-0.05	-0.0727	0.0632	0.1287	0.0349	0.1141	-0.0203	-0.0133	0.2123	0.0277	0.1247	-6.654	5.7145	31.0021
23	0.0324	-0.0347	-0.088	0.0561	0.138	0.3299	0.1013	-0.3767	-0.0858	-0.2191	0.1814	-0.2159	-0.1084	0.0839	0.0338	0.166	-0.0389	0.0219	0.2894	0.0555	0.2896	40.0314	43.2131	54.7665
24	0.5232	-0.01	-0.4039	0.1987	0.211	0.5416	0.0379	-0.1806	-0.3112	0.0668	0.079	0.0005	0.1101	0.1881	0.2891	0.1166	0.0866	-0.0371	0.1554	0.1845	0.495	37.5557	27.2453	47.7421
25	0.9714	-0.4792	-0.2792	0.5359	-0.0869	0.2764	-0.0108	-0.3908	-0.2649	-0.0156	0.0361	-0.174	0.0406	0.3015	0.1444	0.055	-0.022	-0.0439	0.2981	0.0998	0.1202	33.8048	39.1142	57.1596
26	0.1023	-0.0797	0.0107	0.1394	-0.0798	0.0512	0.0836	-0.5034	0.0337	0.1307	-0.0351	0.113	-0.1734	-0.0963	0.026	0.2034	-0.0537	0.0112	0.3598	-0.0136	0.1324	29.851	47.5547	60.3144
27	0.0242	-0.0031	-0.0277	0.0062	-0.0021	0.0346	0.2042	0.0735	-0.2374	0.0072	0.0119	-0.0264	-0.0424	0.0497	0.0064	0.1244	0.0262	-0.0143	0.1399	0.0229	0.1686	33.6184	34.345	45.0263
28	0.4425	0.1711	0.2222	0.3774	-0.0783	0.2132	0.0536	-0.0243	-0.6867	-0.1643	-0.1071	-0.1742	0.2926	0.2145	-0.0478	0.1798	0.0219	-0.0441	0.1712	0.0891	0.3484	28.2502	27.1855	44.4187
29	0.2786	-0.1679	-0.247	1.167	0.961	1.0065	0.0311	-0.1188	-0.1373	-0.0352	0.2437	-0.115	0.016	0.2885	0.2753	0.1135	-0.0078	-0.0981	0.4497	0.1779	0.2856	42.323	36.9464	57.8341
30	0.1289	-0.4405	0.187	1.5845	-0.4134	1.3001	0.158	-0.4339	-0.2418	-0.0053	0.3296	-0.2041	0.2493	-0.0825	0.3996	0.1721	-0.0066	-0.1274	0.5003	0.1538	0.3618	45.1201	38.791	59.6781

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 695 THROUGH 705 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 706 THROUGH 718 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 719 THROUGH 746 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 747 THROUGH 759 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 760 THROUGH 770 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 771 THROUGH 801 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 802 THROUGH 816 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 817 THROUGH 824 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 825 THROUGH 835 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 695 THROUGH 746 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 747 THROUGH 770 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 771 THROUGH 801 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 802 THROUGH 816 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 817 THROUGH 824 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 825 THROUGH 835 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 695 THROUGH 746 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 747 THROUGH 770 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 771 THROUGH 796 )
19	X-RAY DIFFRACTION	19	CHAIN 'C' AND (RESID 797 THROUGH 801 )
20	X-RAY DIFFRACTION	20	CHAIN 'C' AND (RESID 802 THROUGH 816 )
21	X-RAY DIFFRACTION	21	CHAIN 'C' AND (RESID 817 THROUGH 824 )
22	X-RAY DIFFRACTION	22	CHAIN 'C' AND (RESID 825 THROUGH 835 )
23	X-RAY DIFFRACTION	23	CHAIN 'D' AND (RESID 695 THROUGH 705 )
24	X-RAY DIFFRACTION	24	CHAIN 'D' AND (RESID 706 THROUGH 718 )
25	X-RAY DIFFRACTION	25	CHAIN 'D' AND (RESID 719 THROUGH 770 )
26	X-RAY DIFFRACTION	26	CHAIN 'D' AND (RESID 771 THROUGH 796 )
27	X-RAY DIFFRACTION	27	CHAIN 'D' AND (RESID 797 THROUGH 801 )
28	X-RAY DIFFRACTION	28	CHAIN 'D' AND (RESID 802 THROUGH 816 )
29	X-RAY DIFFRACTION	29	CHAIN 'D' AND (RESID 817 THROUGH 824 )
30	X-RAY DIFFRACTION	30	CHAIN 'D' AND (RESID 825 THROUGH 835 )

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