PDB-5xeb: Structure of the envelope glycoprotein of Dhori virus

ID or keywords:

Entry

Database: PDB / ID: 5xeb

Title

Structure of the envelope glycoprotein of Dhori virus

Components

Envelope glycoprotein

Keywords

VIRAL PROTEIN / Dhori virus / glycoprotein / fuion machine

Function / homology

Baculovirus Gp64, envelope glycoprotein / Baculovirus gp64 envelope glycoprotein family / modulation by virus of host process / viral envelope / virion membrane / membrane / Envelope glycoprotein

Function and homology information

Biological species

Dhori virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.497 Å

Authors

Peng, R. / Shi, Y. / Qi, J. / Gao, G.F.

Funding support

China, 1items

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structures of human-infectingThogotovirusfusogens support a common ancestor with insect baculovirus
Authors: Peng, R. / Zhang, S. / Cui, Y. / Shi, Y. / Gao, G.F. / Qi, J.

History

Deposition	Apr 3, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 4, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: 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 1.2	Jun 13, 2018	Group: Data collection / Database references / Structure summary Category: citation / struct_keywords Item: _citation.title / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.3	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5xeb.cif.gz	483.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5xeb.ent.gz	401.6 KB	Display	PDB format
PDBx/mmJSON format	5xeb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5xeb_validation.pdf.gz	477.3 KB	Display	wwPDB validaton report
Full document	5xeb_full_validation.pdf.gz	506.8 KB	Display
Data in XML	5xeb_validation.xml.gz	45.7 KB	Display
Data in CIF	5xeb_validation.cif.gz	62.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xe/5xeb ftp://data.pdbj.org/pub/pdb/validation_reports/xe/5xeb	HTTPS FTP

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Related structure data

Related structure data	5xeaC C: citing same article (ref.)
Similar structure data	5zl2-3 5zkx-1 2vde-d 1ek9-d 5zl2-2 5xea-d 5zkx-2 5zl2-1 1tqq-d 5zkx-3 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

Related structure data

5xeaC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Envelope glycoprotein

B: Envelope glycoprotein

C: Envelope glycoprotein

hetero molecules

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

1

A: Envelope glycoprotein

hetero molecules

A: Envelope glycoprotein

hetero molecules

A: Envelope glycoprotein

hetero molecules

defined by author&software
Evidence: gel filtration
162 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Envelope glycoprotein

hetero molecules

B: Envelope glycoprotein

hetero molecules

B: Envelope glycoprotein

hetero molecules

defined by author&software
161 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Envelope glycoprotein

hetero molecules

C: Envelope glycoprotein

hetero molecules

C: Envelope glycoprotein

hetero molecules

defined by author&software
161 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	106.729, 106.729, 134.440
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	143
Space group name H-M	P3

Components on special symmetry positions

ID	Model	Components
1	1	A-800- HOH
2	1	B-753- HOH

#1: Protein

Envelope glycoprotein

Mass: 53599.336 Da / Num. of mol.: 3 / Fragment: UNP residues 21-494
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Dhori virus (strain Indian/1313/61) / Strain: Indian/1313/61 / Gene: P4 / Cell line (production host): High Five / Production host:

Baculovirus expression vector pFastBac1-HM / References: UniProt: P27427

#2: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.75 Å³/Da / Density % sol: 55.26 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 6% v/v Ethylene glycol, 0.1 M Citric acid pH 3.5, 10% w/v Polyethylene glycol 6.000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97845 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97845 Å / Relative weight: 1
Reflection	Resolution: 2.49→50 Å / Num. obs: 59514 / % possible obs: 99.9 % / Redundancy: 8.5 % / R_merge(I) obs: 0.15 / Net I/σ(I): 14.492
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 8.4 % / R_merge(I) obs: 2.113 / Mean I/σ(I) obs: 1.078 / Num. unique obs: 5937 / % possible all: 99.8

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.497→34.935 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 36.5

	R_factor	Num. reflection	% reflection
R_free	0.2571	2170	5.04 %
R_work	0.231	-	-
obs	0.2311	43023	72.32 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.497→34.935 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9336	0	56	201	9593

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	9657
X-RAY DIFFRACTION	f_angle_d	0.706	13120
X-RAY DIFFRACTION	f_dihedral_angle_d	14.824	5744
X-RAY DIFFRACTION	f_chiral_restr	0.043	1436
X-RAY DIFFRACTION	f_plane_restr	0.005	1651

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 (%)
2.4967-2.5547	0.4118	40	0.3331	861	X-RAY DIFFRACTION	23
2.5547-2.6186	0.418	53	0.2791	997	X-RAY DIFFRACTION	26
2.6186-2.6894	0.3233	52	0.2758	1200	X-RAY DIFFRACTION	31
2.6894-2.7685	0.3254	89	0.2711	1347	X-RAY DIFFRACTION	36
2.7685-2.8578	0.2732	110	0.2792	1658	X-RAY DIFFRACTION	45
2.8578-2.9599	0.3534	116	0.2903	2029	X-RAY DIFFRACTION	54
2.9599-3.0783	0.4066	134	0.2744	2639	X-RAY DIFFRACTION	70
3.0783-3.2183	0.283	190	0.2686	3746	X-RAY DIFFRACTION	99
3.2183-3.3879	0.3115	197	0.2536	3716	X-RAY DIFFRACTION	100
3.3879-3.5999	0.2806	227	0.2491	3792	X-RAY DIFFRACTION	100
3.5999-3.8776	0.3071	184	0.2287	3770	X-RAY DIFFRACTION	100
3.8776-4.2672	0.2871	188	0.2294	3800	X-RAY DIFFRACTION	100
4.2672-4.8832	0.2455	208	0.2132	3760	X-RAY DIFFRACTION	100
4.8832-6.1469	0.2703	202	0.2622	3763	X-RAY DIFFRACTION	100
6.1469-34.9387	0.3388	180	0.291	3775	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	0.0894	-0.0592	0.3277	0.2751	0.1422	0.8293	-0.0992	0.0487	-0.0333	0.0323	0.0677	-0.0371	-0.4945	0.5014	-0.2889	0.2172	-0.266	-0.0564	0.334	0.0294	0.1805	12.696	5.3046	-13.8709
2	0.4125	0.0568	-0.0959	0.0706	0.0989	1.6885	-0.2593	0.084	-0.0547	-0.0765	0.0544	-0.174	-0.1674	0.6636	-0.7145	-0.0067	-0.1489	-0.0426	0.3075	-0.0407	0.2066	19.781	0.0842	0.9897
3	0.1468	0.0456	0.0878	0.1718	-0.4353	1.295	-0.1655	-0.1055	0.0586	0.3068	0.1503	0.0538	-0.3442	-0.0207	-0.0277	-0.103	-0.1845	0.0159	-0.0131	-0.0284	0.0978	-0.4883	4.5486	29.9803
4	1.9593	0.4565	-1.0812	2.382	-0.556	2.285	-0.0504	0.4113	-0.0964	-0.2055	0.0075	-0.0997	0.12	0.3468	0.2164	0.3531	0.1189	0.138	0.5325	-0.0569	0.2659	68.6661	25.3397	-34.4541
5	0.2754	0.095	0.4129	0.169	0.1607	0.5919	-0.127	-0.4147	-0.1469	0.2011	-0.0648	0.1756	0.3183	-0.7447	-0.1164	0.1013	-0.3157	0.028	0.247	-0.0084	0.1119	39.6004	18.0489	34.9383
6	0.1431	-0.0237	-0.0014	0.1398	0.235	0.3635	0.1135	0.0355	-0.0485	0.0919	0.0124	0.0345	0.1834	0.0848	-0.2793	-0.003	0.0872	-0.026	0.0367	-0.017	0.1846	56.1356	27.0275	-4.2165
7	0.095	-0.0223	0.3451	0.0829	-0.1381	2.2495	0.032	-0.039	0.0457	-0.0398	-0.008	0.0424	-0.4208	-0.7439	0.1478	0.3003	0.0201	0.0115	0.2302	-0.0261	0.2005	44.8374	32.7075	-5.5749
8	1.0914	0.4319	0.6981	1.4555	-0.3244	1.05	-0.3739	0.7388	0.1373	-0.3863	0.1017	-0.0529	0.4561	-0.1921	-0.0024	0.5881	-0.3292	-0.0792	0.8641	0.1104	0.7218	40.1705	-39.8696	-104.9029
9	0.1977	0.1082	-0.3367	0.4882	-0.7751	1.3398	-0.1141	-0.1753	0.1599	0.237	-0.3096	-0.2592	-1.6147	0.2583	-0.168	1.4003	0.0516	-0.1285	0.6217	-0.0626	0.8785	52.4431	-11.8384	-25.5615
10	0.0867	-0.0902	0.2416	0.1643	-0.639	2.7622	0.0508	-0.1706	-0.0567	-0.1218	-0.0596	-0.1178	-0.822	-0.168	0.0319	1.1422	-0.1785	-0.1186	0.615	0.0262	0.7678	58.5394	-14.2263	-14.8927
11	0.649	0.0018	-0.4796	1.6949	-0.6568	0.6079	-0.2218	-0.3107	0.3196	0.2764	-0.1256	-0.29	-1.0475	-0.1411	0.1498	1.2824	0.2761	-0.0698	0.6032	0.0361	0.9263	44.3006	-10.1319	-43.0807
12	0.0711	0.0004	-0.3335	0.0347	0.0395	1.7931	-0.1239	0.2664	0.3454	-0.1334	-0.3513	-0.1791	-0.2847	0.403	0.1601	1.5577	-0.1717	-0.097	0.8099	-0.003	0.9881	45.1883	-8.1691	-65.2019
13	4.5771	0.6693	-0.381	1.971	-0.3954	0.9141	-0.0898	0.265	0.1768	0.1605	-0.3186	-0.0131	-0.6434	-0.8448	0.1115	0.6635	0.1141	-0.0121	0.6673	0.0671	0.7724	39.7173	-18.9374	-69.4828
14	0.6021	0.0799	0.3827	0.0111	0.0497	0.2405	0.0797	0.1052	0.1764	-0.0484	0.1372	0.2007	-0.3427	-0.42	0.2982	0.6306	0.3311	-0.1784	0.6688	0.038	1.0927	38.3476	-17.3085	-58.2163
15	0.8936	0.163	0.3947	0.165	0.2551	1.7414	-0.0838	0.2799	0.0379	-0.0294	-0.1854	-0.166	-0.2112	0.1609	-0.0017	0.5201	-0.1028	0.0002	0.3542	-0.0071	0.7253	57.5001	-30.2913	-92.9063
16	1.2646	0.4058	0.0075	1.2005	0.5578	1.0444	0.3138	-0.0716	-0.0033	-0.8234	-0.0543	-0.106	-0.1117	0.3707	0.0406	0.9147	-0.139	-0.1375	0.5109	0.1354	0.8504	57.7512	-23.3028	-26.5928

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 153 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 154 through 310 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 311 through 472 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 24 through 44 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 45 through 287 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 288 through 354 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 355 through 472 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 25 through 45 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 46 through 129 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 130 through 168 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 169 through 212 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 213 through 231 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 232 through 277 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 278 through 310 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 311 through 448 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 449 through 472 )

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