PDB-5t9y: Crystal structure of the infectious salmon anemia virus (ISAV) he...

ID or keywords:

Entry

Database: PDB / ID: 5t9y

Title

Crystal structure of the infectious salmon anemia virus (ISAV) hemagglutinin-esterase protein

Components

HE protein

Keywords

VIRAL PROTEIN / 4-0-acetylsialic acid /

hydrolase /

hemagglutinin /

coiled-coil / viral receptor-complex / infectious salmon anemia virus / ISAV

Function / homology

Haemagglutinin-esterase glycoprotein, infectious salmon anaemia virus-type / Infectious salmon anaemia virus haemagglutinin /

membrane /

FORMIC ACID / HE protein

Function and homology information

Biological species

Infectious salmon anemia virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD /

molecular replacement / Resolution: 1.8 Å

Authors

Cook, J.D. / Sultana, A. / Lee, J.E.

Funding support

Canada, 1items

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of the infectious salmon anemia virus receptor complex illustrates a unique binding strategy for attachment.
Authors: Cook, J.D. / Sultana, A. / Lee, J.E.

History

Deposition	Sep 9, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Apr 5, 2017	Group: Database references
Revision 1.2	Apr 19, 2017	Group: Database references
Revision 1.3	Sep 27, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5t9y.cif.gz	555.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5t9y.ent.gz	481.1 KB	Display	PDB format
PDBx/mmJSON format	5t9y.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/t9/5t9y ftp://data.pdbj.org/pub/pdb/validation_reports/t9/5t9y	HTTPS FTP

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Related structure data

Related structure data	5t96C C: citing same article (ref.)
Similar structure data	5t96-2 2rhp-d 1yo8-d 1ujw-d 1g5g-2 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	#76 - Apr 2006 Hemagglutinin similarity (1)

Deposited unit

A: HE protein

B: HE protein

C: HE protein

hetero molecules

116 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	142.419, 93.289, 96.722
Angle α, β, γ (deg.)	90.00, 122.01, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-832- HOH
2	1	B-898- HOH

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Protein , 1 types, 3 molecules ABC

#1: Protein	HE protein / Hemagglutinin / Hemagglutinin-esterase glycoprotein Mass: 37528.578 Da / Num. of mol.: 3 / Fragment: UNP residues 17-353 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Infectious salmon anemia virus / Gene: HE / Plasmid: pMT-puro / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9J0Y0

#1: Protein

HE protein / Hemagglutinin / Hemagglutinin-esterase glycoprotein

Mass: 37528.578 Da / Num. of mol.: 3 / Fragment: UNP residues 17-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Infectious salmon anemia virus / Gene: HE / Plasmid: pMT-puro / Cell line (production host): S2 / Production host:

Drosophila melanogaster (fruit fly) / References: UniProt: Q9J0Y0

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Non-polymers , 5 types, 1217 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	... ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: CH₂O₂
#5: Chemical	ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆₉H₁₄₀O₃₅ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1187 / 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: 2.59 Å³/Da / Density % sol: 52.48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: [0.2 M] magnesium formate, 20% PEG 3350, w/ a [0.8 M] sodium phosphate, [0.8 M] potassium phosphate, [0.1 M] HEPES pH 7.5 solution as a 1:6 ratio drop additive

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.97949 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 28, 2016 / Details: 9 CCDS, 9 TILED FIBER-OPTIC TAPERS

Radiation

Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9795	1
2	0.97949	1

Reflection

Resolution: 1.8→47.72 Å / Num. obs: 99190 / % possible obs: 99.9 % / Redundancy: 4.2 % / B_iso Wilson estimate: 21.18 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.057 / Net I/σ(I): 15.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	CC_1/2	Diffraction-ID	% possible all
1.8-1.83	4.2	0.498	0.846	1	100
9.86-47.72	3.9	0.029	0.998	1	98.7

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	7.77 Å	47.61 Å
Translation	7.77 Å	47.61 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
Aimless	0.5.17	data scaling
Coot		model building
PDB_EXTRACT	3.2	data extraction
XDS		data reduction
PHASER	2.6.0	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.8→47.72 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1677	2000	2.02 %	Random selection
R_work	0.1367	-	-	-
obs	0.1373	99183	99.92 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→47.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7276	0	100	1187	8563

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7605
X-RAY DIFFRACTION	f_angle_d	0.988	10330
X-RAY DIFFRACTION	f_dihedral_angle_d	12.086	4596
X-RAY DIFFRACTION	f_chiral_restr	0.061	1197
X-RAY DIFFRACTION	f_plane_restr	0.007	1332

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 (%)
1.8-1.845	0.223	142	0.1935	6917	X-RAY DIFFRACTION	100
1.845-1.8949	0.1829	143	0.1739	6958	X-RAY DIFFRACTION	100
1.8949-1.9507	0.1939	142	0.159	6879	X-RAY DIFFRACTION	100
1.9507-2.0136	0.1918	143	0.1493	6944	X-RAY DIFFRACTION	100
2.0136-2.0856	0.171	141	0.1478	6889	X-RAY DIFFRACTION	100
2.0856-2.1691	0.1507	144	0.1347	6941	X-RAY DIFFRACTION	100
2.1691-2.2678	0.1712	142	0.1329	6908	X-RAY DIFFRACTION	100
2.2678-2.3874	0.1389	142	0.13	6915	X-RAY DIFFRACTION	100
2.3874-2.537	0.1617	144	0.1299	6975	X-RAY DIFFRACTION	100
2.537-2.7328	0.1588	143	0.1323	6934	X-RAY DIFFRACTION	100
2.7328-3.0078	0.1683	143	0.1377	6952	X-RAY DIFFRACTION	100
3.0078-3.4429	0.1964	143	0.1394	6971	X-RAY DIFFRACTION	100
3.4429-4.3373	0.1547	142	0.1225	6938	X-RAY DIFFRACTION	100
4.3373-47.7371	0.1587	146	0.1333	7062	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	1.9249	0.3423	-0.1182	2.0929	-1.0269	1.4857	0.0306	-0.0615	0.1484	0.0293	-0.0162	0.2245	-0.2547	-0.3376	-0.001	0.1885	0.0762	-0.045	0.2206	-0.043	0.1919	24.1541	12.0012	3.2108
2	1.8844	-0.4284	-0.3107	0.7057	0.2541	1.0686	0.0182	0.0279	-0.042	-0.1522	-0.0331	-0.0188	-0.0337	-0.0062	0.0173	0.1866	0.0082	-0.013	0.1209	-0.009	0.1554	44.6351	0.6666	-2.1702
3	1.1904	-0.2797	0.1261	0.6547	-0.0517	0.8701	0.0481	0.1514	-0.0941	-0.1904	-0.0693	0.0627	0.0187	-0.0992	0.0182	0.2062	0.0085	-0.025	0.1664	-0.0373	0.1691	38.748	0.1615	-8.0788
4	2.0601	-0.1543	-0.3767	5.0812	-3.2314	3.5975	0.0709	-0.143	0.0075	0.1323	0.0713	0.5483	-0.2439	-0.6769	-0.1904	0.1667	0.0543	-0.0514	0.4461	-0.0627	0.3195	13.8824	7.2333	3.9131
5	5.5802	-0.3244	-3.9026	1.7255	0.3572	2.7365	0.0443	0.0369	-0.0595	-0.0454	0.2043	0.37	-0.0738	-0.3691	-0.1084	0.1881	0.0145	-0.0259	0.7266	-0.0255	0.5323	3.2457	3.1722	12.1731
6	5.1186	2.5696	-2.951	2.0256	-1.3821	1.7162	0.5602	-0.5173	0.9624	0.5727	-0.7945	0.3469	-0.0228	0.1809	-0.1782	0.3974	-0.1491	0.1324	0.9094	-0.0283	0.6426	-32.1061	5.8181	32.505
7	1.789	0.245	0.5624	1.5896	-0.1649	1.8375	-0.0147	-0.1486	-0.0216	0.1378	-0.0098	0.1417	-0.0769	-0.3168	0.0198	0.1868	0.0334	0.03	0.2238	-0.0179	0.1525	30.3028	9.0954	31.7615
8	1.0873	-0.209	-0.4373	0.6059	0.1749	1.1578	-0.003	-0.0777	0.1007	0.0033	0.001	-0.0619	-0.2876	0.0404	-0.0109	0.2335	-0.0095	-0.0183	0.1207	-0.0095	0.1619	48.0074	17.4182	20.3363
9	1.4935	-0.4735	-0.2089	1.4582	0.1391	4.7429	-0.0204	-0.1993	-0.0871	0.0784	0.0537	0.3271	-0.0955	-0.7686	0.0211	0.2177	0.0875	0.0308	0.4027	-0.0001	0.2835	19.8324	13.2701	30.3173
10	6.7031	2.1085	-1.3816	0.9853	-0.1847	0.4254	0.1361	-0.8091	-0.5189	0.1727	0.0711	0.1308	0.1962	-0.2724	0.0256	0.3718	-0.0086	-0.018	1.0139	0.4032	0.651	-14.8368	2.0224	31.2962
11	0.944	-0.4624	-0.1993	1.7258	0.186	1.1548	-0.0563	0.0278	-0.1198	0.0271	-0.0392	0.3224	0.1644	-0.3876	0.092	0.196	-0.0777	0.0092	0.2589	-0.0186	0.2602	25.9195	-14.867	15.3124
12	0.8747	-0.1351	-0.0873	0.5138	-0.0306	0.8717	0.0109	-0.0617	-0.047	0.0369	-0.0308	0.0231	0.1321	-0.0177	0.0222	0.1795	-0.0221	0.0025	0.1272	0.015	0.1586	45.4299	-11.8668	20.9899
13	1.7788	-0.3727	-0.5883	1.4152	0.3729	1.7254	-0.0037	-0.0303	-0.0217	-0.036	-0.0236	-0.0829	0.1304	0.113	0.0235	0.1765	-0.0022	-0.0094	0.1885	0.0413	0.1732	60.3261	-8.5582	17.7324
14	1.4203	1.097	-0.8564	2.0147	1.0751	3.0993	-0.0346	-0.2296	-0.4133	0.1418	-0.0091	-0.2625	0.1992	0.4866	0.0463	0.1967	0.0248	-0.0016	0.2192	0.0831	0.2394	63.7763	-14.5035	24.1872
15	0.8332	0.0516	-0	0.8436	-0.0069	1.0605	-0.0179	-0.0924	-0.1667	0.1079	-0.0295	0.0737	0.276	-0.0917	0.0298	0.2162	-0.0321	0.0241	0.1465	0.0227	0.1629	41.3314	-17.3488	25.2166
16	1.257	1.4983	0.9423	2.2804	0.4122	1.7694	-0.0976	-0.078	-0.0086	-0.0337	-0.0224	0.5778	0.0676	-0.606	0.0876	0.1882	-0.1049	0.0712	0.4215	-0.0239	0.3568	17.2193	-13.335	22.4661
17	6.0939	-2.4772	1.122	1.7008	-0.4333	0.208	0.0409	0.2206	-0.1063	-0.0273	-0.1143	0.6855	0.0483	-0.6	-0.0237	0.2787	-0.0412	0.0533	0.7723	0.0085	0.6333	6.0278	-6.3988	25.5104
18	7.228	-2.6281	-3.3682	5.9228	1.3631	6.2797	0.2074	0.8001	-0.6712	-0.0364	-0.5248	0.121	0.299	-0.1602	0.3279	0.3878	-0.0499	-0.0316	0.5675	0.1823	0.6499	-32.2316	-1.1684	25.1018

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 17 through 56 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 57 through 169 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 170 through 266 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 267 through 290 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 291 through 306 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 307 through 337 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 17 through 56 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 57 through 266 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 267 through 290 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 291 through 335 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 17 through 56 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 57 through 140 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 141 through 169 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 170 through 188 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 189 through 266 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 267 through 290 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 291 through 306 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 307 through 335 )

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