PDB-8yhv: Structure of the VP40 from Biortus.

ID or keywords:

Entry

Database: PDB / ID: 8yhv

Title

Structure of the VP40 from Biortus.

Components

Matrix protein VP40

Keywords

VIRAL PROTEIN / Ribonucleoprotein / RNA-binding / Suppressor of RNA silencing

Function / homology

Function and homology information

host cell endomembrane system / host cell late endosome membrane / viral budding via host ESCRT complex / structural constituent of virion / symbiont-mediated suppression of host innate immune response / ribonucleoprotein complex / host cell plasma membrane / virion membrane / RNA binding / extracellular region / membrane
Similarity search - Function

Biological species

Zaire ebolavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Zhang, B.

Funding support

1items

Citation

Journal: To Be Published
Title: Structure of the VP40 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Zhang, B.

History

Deposition	Feb 28, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Mar 13, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8yhv.cif.gz	66.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8yhv.ent.gz	45 KB	Display	PDB format
PDBx/mmJSON format	8yhv.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/yh/8yhv ftp://data.pdbj.org/pub/pdb/validation_reports/yh/8yhv	HTTPS FTP

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Related structure data

Similar structure data	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	#178 - Oct 2014 Ebola Virus Proteins similarity (5)

Deposited unit

A: Matrix protein VP40

31.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Matrix protein VP40

defined by author&software
Evidence: gel filtration
63.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Matrix protein VP40

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

Unit cell

Length a, b, c (Å)	65.031, 90.812, 49.220
Angle α, β, γ (deg.)	90.000, 97.816, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Matrix protein VP40 / Ebola VP40 / eVP40 / Membrane-associated protein VP40 Mass: 31860.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zaire ebolavirus (strain Kikwit-95) / Gene: VP40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q77DJ6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.26 Å³/Da / Density % sol: 45.57 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Magnesium chloride hexahydrate 0.1M Tris pH8.5, 25% PEG4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.35→48.76 Å / Num. obs: 11721 / % possible obs: 99.1 % / Redundancy: 4.1 % / R_merge(I) obs: 0.076 / Net I/σ(I): 10.9
Reflection shell	Resolution: 2.35→2.43 Å / R_merge(I) obs: 0.616 / Num. unique obs: 1136

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.35→45.447 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.928 / SU B: 8.239 / SU ML: 0.187 / Cross valid method: FREE R-VALUE / ESU R: 0.329 / ESU R Free: 0.226
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2229	566	4.829 %
R_work	0.1739	11154	-
all	0.176	-	-
obs	-	11720	98.911 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 43.518 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.669 Å²	0 Å²	-1.574 Å²
2-	-	-2.31 Å²	-0 Å²
3-	-	-	1.997 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→45.447 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1884	0	0	102	1986

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	1935
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1938
X-RAY DIFFRACTION	r_angle_refined_deg	1.215	1.822	2644
X-RAY DIFFRACTION	r_angle_other_deg	0.393	1.744	4494
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.35	5	241
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.608	5	7
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.203	10	325
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.025	10	66
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	321
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2136
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	368
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	310
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	1664
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	920
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	1004
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	90
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.157	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.078	0.2	50
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.227	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	2.742	4.375	976
X-RAY DIFFRACTION	r_mcbond_other	2.737	4.376	976
X-RAY DIFFRACTION	r_mcangle_it	4.401	7.805	1210
X-RAY DIFFRACTION	r_mcangle_other	4.401	7.808	1211
X-RAY DIFFRACTION	r_scbond_it	2.993	4.721	959
X-RAY DIFFRACTION	r_scbond_other	2.992	4.724	960
X-RAY DIFFRACTION	r_scangle_it	4.994	8.496	1433
X-RAY DIFFRACTION	r_scangle_other	4.992	8.498	1434
X-RAY DIFFRACTION	r_lrange_it	7.611	39.796	1985
X-RAY DIFFRACTION	r_lrange_other	7.6	39.654	1967

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.35-2.411	0.245	36	0.259	831	0.259	880	0.957	0.95	98.5227	0.238
2.411-2.477	0.309	29	0.25	784	0.252	825	0.944	0.959	98.5455	0.23
2.477-2.548	0.248	34	0.247	791	0.247	836	0.933	0.96	98.6842	0.219
2.548-2.627	0.315	43	0.222	742	0.227	797	0.93	0.967	98.4944	0.198
2.627-2.712	0.295	35	0.218	732	0.222	776	0.932	0.969	98.8402	0.188
2.712-2.807	0.28	31	0.186	711	0.19	751	0.961	0.977	98.8016	0.158
2.807-2.913	0.246	46	0.176	677	0.18	731	0.959	0.981	98.9056	0.153
2.913-3.031	0.196	35	0.163	650	0.165	691	0.975	0.983	99.1317	0.146
3.031-3.165	0.222	35	0.162	625	0.165	669	0.966	0.986	98.6547	0.149
3.165-3.319	0.241	29	0.162	616	0.164	651	0.956	0.987	99.0783	0.153
3.319-3.498	0.195	27	0.165	590	0.166	623	0.969	0.987	99.0369	0.158
3.498-3.708	0.248	33	0.159	529	0.163	567	0.969	0.987	99.1182	0.154
3.708-3.963	0.211	20	0.162	520	0.165	545	0.976	0.986	99.0826	0.162
3.963-4.277	0.205	32	0.144	479	0.148	514	0.973	0.988	99.4163	0.148
4.277-4.682	0.188	25	0.131	441	0.134	470	0.982	0.99	99.1489	0.14
4.682-5.227	0.199	25	0.137	387	0.141	413	0.975	0.99	99.7579	0.152
5.227-6.023	0.197	23	0.2	355	0.199	379	0.979	0.981	99.7361	0.206
6.023-7.344	0.232	10	0.19	311	0.191	323	0.96	0.981	99.3808	0.199
7.344-10.253	0.167	7	0.145	245	0.146	255	0.951	0.985	98.8235	0.171
10.253-45.447	0.212	11	0.224	139	0.223	152	0.971	0.968	98.6842	0.257

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