PDB-5eqw: Structure of the major structural protein D135 of Acidianus taile...

ID or keywords:

Entry

Database: PDB / ID: 5eqw

Title

Structure of the major structural protein D135 of Acidianus tailed spindle virus (ATSV)

Components

Putative major coat protein

Keywords

STRUCTURAL PROTEIN / Archaeal virus / four helix bundle / large tailed spindle virus

Function / homology

RIP/P131 family / viral capsid / NITRATE ION / Putative major coat protein

Function and homology information

Biological species

Acidianus tailed spindle virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.679 Å

Authors

Hochstein, R.A. / Lintner, N.G. / Young, M.J. / Lawrence, C.M.

Funding support

United States, 3items

Organization	Grant number	Country
National Science Foundation (NSF, United States)	DEB-4W4596	United States
National Science Foundation (NSF, United States)	MCB-1413534	United States
National Science Foundation (NSF, United States)	MCB-0920312	United States

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural studies ofAcidianustailed spindle virus reveal a structural paradigm used in the assembly of spindle-shaped viruses.
Authors: Hochstein, R. / Bollschweiler, D. / Dharmavaram, S. / Lintner, N.G. / Plitzko, J.M. / Bruinsma, R. / Engelhardt, H. / Young, M.J. / Klug, W.S. / Lawrence, C.M.

History

Deposition	Nov 13, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 16, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Feb 14, 2018	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3	Apr 18, 2018	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_PubMed / _citation.title / _citation_author.name
Revision 1.4	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Nov 6, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5eqw.cif.gz	269.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5eqw.ent.gz	221.7 KB	Display	PDB format
PDBx/mmJSON format	5eqw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5eqw_validation.pdf.gz	457.2 KB	Display	wwPDB validaton report
Full document	5eqw_full_validation.pdf.gz	457.8 KB	Display
Data in XML	5eqw_validation.xml.gz	30.3 KB	Display
Data in CIF	5eqw_validation.cif.gz	44.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eq/5eqw ftp://data.pdbj.org/pub/pdb/validation_reports/eq/5eqw	HTTPS FTP

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Related structure data

Similar structure data	2flt-d 3mf8-d 3fwt-d 6q00-d 5cb9-d 5m9q-d 4ahi-d 7lio-1 5m9p-d 1tsj-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) 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

Deposited unit

A: Putative major coat protein

B: Putative major coat protein

C: Putative major coat protein

D: Putative major coat protein

E: Putative major coat protein

hetero molecules

81.7 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative major coat protein

hetero molecules

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

2

B: Putative major coat protein

hetero molecules

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

3

C: Putative major coat protein

hetero molecules

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

4

D: Putative major coat protein

hetero molecules

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

5

E: Putative major coat protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	97.780, 41.672, 97.690
Angle α, β, γ (deg.)	90.00, 108.64, 90.00
Int Tables number	3
Space group name H-M	P121

Components on special symmetry positions

ID	Model	Components
1	1	B-394- HOH

#1: Protein	Putative major coat protein Mass: 16213.122 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidianus tailed spindle virus / Gene: ATSV_D135 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A125SJ78
#2: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: NO₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.33 Å³/Da / Density % sol: 47.28 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 2.6 Details: Sodium nitrate, sodium acetate, glycerol, acetonitrile

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.95369 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2011
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95369 Å / Relative weight: 1
Reflection	Resolution: 1.679→50 Å / Num. obs: 84697 / % possible obs: 98.7 % / Redundancy: 3.5 % / R_sym value: 0.066 / Net I/σ(I): 16.26

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
Coot	0.8.1	model building
SCALEPACK		data scaling
SOLVE		phasing
DENZO		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.679→38.005 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.216	4217	4.98 %
R_work	0.189	-	-
obs	0.1904	84672	98.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.679→38.005 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4759	0	40	660	5459

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4978
X-RAY DIFFRACTION	f_angle_d	1.003	6757
X-RAY DIFFRACTION	f_dihedral_angle_d	12.709	1929
X-RAY DIFFRACTION	f_chiral_restr	0.044	731
X-RAY DIFFRACTION	f_plane_restr	0.006	931

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 (%)
1.6791-1.6982	0.2709	113	0.2403	2075	X-RAY DIFFRACTION	79
1.6982-1.7182	0.2463	125	0.2338	2478	X-RAY DIFFRACTION	91
1.7182-1.7391	0.2645	125	0.2345	2644	X-RAY DIFFRACTION	95
1.7391-1.7611	0.2477	133	0.2253	2556	X-RAY DIFFRACTION	97
1.7611-1.7843	0.2364	123	0.2291	2710	X-RAY DIFFRACTION	99
1.7843-1.8088	0.2575	143	0.213	2729	X-RAY DIFFRACTION	100
1.8088-1.8346	0.2436	142	0.2116	2634	X-RAY DIFFRACTION	100
1.8346-1.862	0.2123	132	0.2109	2693	X-RAY DIFFRACTION	100
1.862-1.8911	0.2676	139	0.2013	2741	X-RAY DIFFRACTION	100
1.8911-1.9221	0.2175	142	0.1967	2672	X-RAY DIFFRACTION	100
1.9221-1.9552	0.2188	140	0.1872	2701	X-RAY DIFFRACTION	100
1.9552-1.9908	0.1921	136	0.1734	2735	X-RAY DIFFRACTION	100
1.9908-2.0291	0.192	149	0.1787	2647	X-RAY DIFFRACTION	100
2.0291-2.0705	0.1874	145	0.1801	2741	X-RAY DIFFRACTION	100
2.0705-2.1155	0.2268	129	0.187	2713	X-RAY DIFFRACTION	100
2.1155-2.1647	0.2041	154	0.1867	2713	X-RAY DIFFRACTION	100
2.1647-2.2188	0.2122	134	0.1905	2716	X-RAY DIFFRACTION	100
2.2188-2.2788	0.1965	148	0.1814	2685	X-RAY DIFFRACTION	100
2.2788-2.3458	0.1981	149	0.1775	2715	X-RAY DIFFRACTION	100
2.3458-2.4216	0.2287	148	0.1873	2717	X-RAY DIFFRACTION	100
2.4216-2.5081	0.2416	142	0.1922	2705	X-RAY DIFFRACTION	100
2.5081-2.6085	0.1965	159	0.1903	2734	X-RAY DIFFRACTION	100
2.6085-2.7272	0.257	125	0.1965	2749	X-RAY DIFFRACTION	100
2.7272-2.8709	0.2087	137	0.1883	2704	X-RAY DIFFRACTION	100
2.8709-3.0507	0.2116	138	0.195	2747	X-RAY DIFFRACTION	100
3.0507-3.2861	0.2277	147	0.1861	2705	X-RAY DIFFRACTION	100
3.2861-3.6166	0.2204	174	0.1799	2721	X-RAY DIFFRACTION	100
3.6166-4.1394	0.2029	144	0.1608	2762	X-RAY DIFFRACTION	100
4.1394-5.213	0.2059	150	0.1739	2764	X-RAY DIFFRACTION	99
5.213-38.0144	0.203	152	0.2126	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	4.1026	-3.1887	-0.1317	5.0605	1.1951	3.0017	0.0536	0.2206	0.2037	0.0048	-0.1196	-0.2092	-0.0234	0.1227	0.0341	0.1209	-0.0283	-0.0421	0.1551	0.0437	0.0974	29.3832	66.4002	27.6967
2	3.4314	1.4092	1.6456	2.653	0.0225	3.0636	0.2128	0.3765	-0.4191	-0.855	-0.0307	-0.1881	0.3617	0.1272	-0.1902	0.3275	0.0115	-0.0929	0.2322	-0.019	0.1794	24.511	57.5366	19.4323
3	3.8287	-2.9325	-2.3886	3.7753	3.7646	4.0295	0.0966	-0.0558	-0.3495	-0.1488	-0.0975	0.5832	0.0352	-0.3182	0.0806	0.1504	-0.0184	-0.0752	0.1979	0.0374	0.2274	17.6999	60.2041	28.7587
4	2.1309	-0.3187	0.7266	4.4439	-0.7649	4.2792	-0.2203	-0.0226	0.1615	0.1341	0.0876	0.1855	-0.2724	-0.2027	0.145	0.1751	0.0359	-0.047	0.1233	0.0012	0.1445	20.0152	77.8687	28.9792
5	4.5404	-4.1455	-2.5308	4.9935	4.3747	5.2862	-0.0814	-0.1393	-0.2336	0.3045	0.0891	0.1609	0.141	-0.1159	0.0562	0.1732	-0.0294	-0.0302	0.1643	0.0583	0.1283	24.891	58.3385	36.3544
6	6.7427	5.2064	1.5881	4.5585	0.6756	9.1392	-0.1835	0.6345	0.0345	-0.3566	0.2133	-0.8248	-0.0086	0.4593	-0.0164	0.1211	0.0272	-0.0036	0.1973	0.0143	0.2216	39.6017	55.9268	27.0757
7	3.0078	-1.8358	-1.1049	4.1537	1.0935	2.0805	0.0981	0.2033	0.1977	-0.2619	-0.0302	-0.3622	-0.0888	-0.0005	-0.0619	0.0794	-0.0038	0.0356	0.158	0.0047	0.1139	49.5246	49.6223	34.1415
8	5.4533	2.6038	1.7415	4.3058	0.7738	2.8981	-0.1007	0.5044	-0.4925	-0.7953	0.2024	0.0341	0.302	0.031	-0.1468	0.1581	-0.0209	-0.0135	0.2335	-0.0059	0.165	40.7576	40.8087	30.3975
9	0.6136	-1.4136	-1.6339	4.439	6.087	7.9077	-0.069	-0.1266	-0.1985	0.0174	-0.2406	0.3659	0.0953	-0.2651	0.3642	0.0883	0.0031	0.025	0.2007	-0.0011	0.1863	40.6518	43.3811	41.9035
10	5.1371	-0.5197	1.5942	4.4734	-0.6653	3.8602	-0.029	0.0895	0.3693	-0.0781	0.0305	-0.0343	-0.0078	0.0106	0.0082	0.0722	0.0104	0.0103	0.0854	-0.0064	0.0711	42.7764	61.1579	40.5033
11	3.2328	0.3871	0.1671	8.134	5.0737	5.424	-0.167	-0.2231	-0.2351	0.3231	-0.0588	-0.0688	0.269	-0.1291	0.2279	0.0886	0.023	0.0014	0.1318	0.0438	0.1103	51.0033	41.8673	43.8741
12	8.7002	5.39	-2.0193	4.2138	-3.4276	7.5615	0.0211	0.9311	0.4109	-0.6217	0.3529	-0.3559	-0.145	-0.0522	-0.4386	0.2388	0.0235	0.111	0.2553	-0.0199	0.239	57.7287	39.7545	27.3868
13	2.4571	-0.151	0.0782	5.6417	3.3467	3.3876	-0.0039	0.1796	0.1355	-0.3265	-0.0319	-0.1053	-0.1562	0.05	0.0516	0.1425	0.024	0.0788	0.1782	0.0339	0.1734	69.5726	33.027	27.6329
14	4.9776	3.1676	-0.0848	2.3308	-0.6121	3.5081	-0.1364	0.3193	-0.5121	-0.3274	-0.1552	0.0318	0.5816	-0.3588	0.3025	0.2248	-0.0122	0.1134	0.2416	-0.0503	0.313	60.3465	24.1083	29.75
15	3.6295	3.8557	2.6324	7.2916	3.6911	3.0997	-0.1289	-0.4373	-0.0266	1.0106	-0.3054	0.5302	0.498	-0.2533	0.4189	0.29	0.036	0.1091	0.2234	-0.0005	0.2	67.2977	26.8399	39.0931
16	5.9149	-0.6018	0.9568	5.6951	-0.5244	2.4156	0.07	-0.1847	0.4317	0.1753	0.0835	-0.3825	-0.0522	0.0946	-0.1548	0.1415	0.0106	0.0358	0.125	-0.041	0.1919	67.9536	44.4906	36.8544
17	6.5693	4.2679	3.6841	4.9878	5.4613	7.5143	-0.2759	-0.4093	-0.0568	0.1753	0.063	-0.3207	0.1157	0.0208	0.0878	0.2253	0.0766	0.0524	0.2098	0.0168	0.2611	76.6932	25.0383	34.3521
18	9.434	4.9744	-4.4979	5.1316	-6.3962	9.1314	0.0852	0.7228	0.3062	-0.4424	0.0884	0.1346	-0.3537	-0.5409	-0.2318	0.239	0.0311	0.101	0.229	-0.0121	0.2012	72.0013	22.6687	17.6833
19	2.0084	1.4269	1.2806	5.698	3.4536	4.0544	-0.0038	0.1187	0.0625	-0.2188	-0.0652	0.2332	-0.1804	-0.256	0.0581	0.1044	0.0411	0.0353	0.1482	0.0147	0.1025	81.5601	16.4309	10.3095
20	2.8071	2.2758	-1.3521	2.778	-1.3773	4.7236	-0.1031	0.1344	-0.1428	0.1004	-0.0251	0.7257	0.5662	-0.4695	0.1645	0.2351	-0.0191	0.1037	0.2473	-0.0069	0.2499	75.4982	7.598	17.5984
21	6.3727	5.1482	1.9638	4.137	1.6775	1.5671	0.1749	-0.4206	-0.0053	0.6835	-0.2473	0.1661	0.2576	-0.0588	0.042	0.2696	0.0431	0.0359	0.1765	0.0025	0.0928	86.5399	10.209	21.0477
22	3.9668	-0.9108	-0.7038	4.6303	-0.435	2.5535	0.1037	-0.0886	0.1781	0.0744	0.0653	-0.0625	-0.217	0.0057	-0.1601	0.1347	-0.0034	0.049	0.0964	-0.036	0.1477	85.8395	27.9241	18.726
23	5.7519	5.9276	1.8067	9.1509	2.5596	3.1584	0.1897	-0.084	-0.099	0.2833	-0.0285	-0.2401	0.3002	0.0988	-0.1791	0.1459	0.0612	0.0352	0.1423	0.004	0.102	91.2584	8.41	11.5609
24	8.2684	-3.1808	2.3268	3.4957	0.9505	3.1884	-0.1945	0.2026	0.0794	-0.6618	0.3036	0.5596	-0.3343	-0.6608	-0.209	0.22	0.0064	-0.0291	0.2289	0.0014	0.1474	77.6027	5.9691	0.8962
25	1.7611	0.5954	1.0116	2.0804	0.5016	2.0035	-0.1156	0.0481	0.1758	-0.2657	0.0097	0.3529	-0.0903	-0.1579	0.0264	0.1293	0.0226	-0.0758	0.1763	0.0032	0.1382	80.841	-0.4021	-10.8138
26	3.4787	-0.1137	0.2814	2.8968	-0.9216	4.3376	0.0948	-0.3723	-0.4012	0.3227	-0.0548	0.4127	0.4196	-0.378	-0.0583	0.1946	-0.0218	-0.0011	0.2081	0.0211	0.1285	80.2241	-9.1822	-1.2342
27	6.9372	5.0997	-1.3549	3.7035	-1.2874	1.0094	0.3052	-0.184	-0.3217	0.253	-0.208	-0.0291	0.1634	0.1413	-0.0846	0.1597	-0.0011	-0.0734	0.1697	0.0055	0.1289	91.2106	-6.5947	-5.2014
28	2.5958	-0.6828	-1.357	4.7135	0.3349	5.0279	-0.0772	0.0314	0.1135	-0.2044	-0.0108	0.1249	-0.3724	-0.0251	0.0798	0.0962	-0.0225	-0.0309	0.097	-0.0066	0.0923	89.1289	11.2107	-6.7336
29	2.3637	1.7592	-2.4168	2.2996	-2.8841	4.1088	-0.0201	-0.0916	-0.1819	-0.3741	0.0287	-0.1165	0.025	0.2018	-0.0358	0.1987	0.0182	-0.0269	0.1788	-0.0452	0.1744	89.441	-8.3402	-15.6268
30	5.966	-4.2677	3.5425	5.3702	-4.5671	3.9546	-0.2191	-0.5693	-0.0197	-0.2454	0.4263	0.8022	-0.2182	-0.8871	-0.0321	0.2612	-0.0051	-0.1292	0.2845	0.0003	0.2746	71.8151	-10.1394	-16.3916

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 30 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 31 through 49 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 50 through 69 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 70 through 97 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 98 through 118 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 119 through 131 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 10 through 30 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 31 through 49 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 50 through 69 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 70 through 97 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 98 through 118 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 119 through 132 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 10 through 30 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 31 through 49 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 50 through 69 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 70 through 97 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 98 through 118 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 119 through 131 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 10 through 30 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 31 through 49 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 50 through 69 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 70 through 97 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 98 through 118 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 119 through 131 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 10 through 30 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 31 through 49 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 50 through 69 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 70 through 97 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 98 through 118 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 119 through 132 )

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