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- PDB-7jzt: Low resolution crystal structure of Zaire Ebola virus VP40 in spa... -

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Basic information

Entry
Database: PDB / ID: 7jzt
TitleLow resolution crystal structure of Zaire Ebola virus VP40 in space group P6422
ComponentsMatrix protein VP40
KeywordsVIRAL PROTEIN / VP40 / matrix protein / Ebola virus
Function / homology
Function and homology information


intracellular transport of virus / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / viral budding / host cell late endosome membrane / viral budding via host ESCRT complex / host cell membrane / virus-mediated perturbation of host defense response / viral budding from plasma membrane ...intracellular transport of virus / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / viral budding / host cell late endosome membrane / viral budding via host ESCRT complex / host cell membrane / virus-mediated perturbation of host defense response / viral budding from plasma membrane / structural constituent of virion / ribonucleoprotein complex / membrane raft / host cell plasma membrane / virion membrane / RNA binding / extracellular region / identical protein binding
Similarity search - Function
EV matrix protein, C-terminal / EV matrix protein / EV matrix domain superfamily / EV matrix protein, N-terminal / Matrix protein VP40
Similarity search - Domain/homology
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.77 Å
AuthorsNorris, M.J. / Bornholdt, Z.A. / Saphire, E.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI118016 United States
CitationJournal: Elife / Year: 2020
Title: Ebola and Marburg virus matrix layers are locally ordered assemblies of VP40 dimers.
Authors: William Wan / Mairi Clarke / Michael J Norris / Larissa Kolesnikova / Alexander Koehler / Zachary A Bornholdt / Stephan Becker / Erica Ollmann Saphire / John Ag Briggs /
Abstract: Filoviruses such as Ebola and Marburg virus bud from the host membrane as enveloped virions. This process is achieved by the matrix protein VP40. When expressed alone, VP40 induces budding of ...Filoviruses such as Ebola and Marburg virus bud from the host membrane as enveloped virions. This process is achieved by the matrix protein VP40. When expressed alone, VP40 induces budding of filamentous virus-like particles, suggesting that localization to the plasma membrane, oligomerization into a matrix layer, and generation of membrane curvature are intrinsic properties of VP40. There has been no direct information on the structure of VP40 matrix layers within viruses or virus-like particles. We present structures of Ebola and Marburg VP40 matrix layers in intact virus-like particles, and within intact Marburg viruses. VP40 dimers assemble extended chains via C-terminal domain interactions. These chains stack to form 2D matrix lattices below the membrane surface. These lattices form a patchwork assembly across the membrane and suggesting that assembly may begin at multiple points. Our observations define the structure and arrangement of the matrix protein layer that mediates formation of filovirus particles.
History
DepositionSep 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein VP40
B: Matrix protein VP40
C: Matrix protein VP40
D: Matrix protein VP40


Theoretical massNumber of molelcules
Total (without water)128,9774
Polymers128,9774
Non-polymers00
Water0
1
A: Matrix protein VP40
D: Matrix protein VP40


Theoretical massNumber of molelcules
Total (without water)64,4882
Polymers64,4882
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-14 kcal/mol
Surface area25860 Å2
MethodPISA
2
B: Matrix protein VP40
C: Matrix protein VP40


Theoretical massNumber of molelcules
Total (without water)64,4882
Polymers64,4882
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-13 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.275, 105.275, 463.738
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein
Matrix protein VP40 / Ebola VP40 / eVP40 / Membrane-associated protein VP40


Mass: 32244.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: VP40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05128

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.2 M Lithium citrate tribasic tetrahydrate, 20% w/v Polyethylene glycol 3350, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 85 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.77→154.586 Å / Num. obs: 7524 / % possible obs: 90.8 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.05 / Rrim(I) all: 0.15 / Net I/σ(I): 12.3
Reflection shellResolution: 3.77→4.304 Å / Rmerge(I) obs: 1.848 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 376 / Rpim(I) all: 0.561 / Rrim(I) all: 1.931

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.45 Å19.9 Å
Translation4.45 Å19.9 Å

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Processing

Software
NameVersionClassification
XDSMar 15, 2019data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.25data extraction
Coot0.9 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LDB

4ldb


Resolution: 3.77→19.9 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 46.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3454 352 4.75 %
Rwork0.3151 7065 -
obs0.3165 7417 45.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 414.91 Å2 / Biso mean: 176.5741 Å2 / Biso min: 59.34 Å2
Refinement stepCycle: final / Resolution: 3.77→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6795 0 0 0 6795
Num. residues----915
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.77-4.310.3594220.46383623847
4.31-5.410.3724700.38911805187535
5.41-19.90.34122600.29894898515891
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.08190.87140.00942.1369-0.358.52740.8237-0.65790.6922-0.7216-1.2031.03121.10952.60070.12920.2899-0.4068-0.7951.30270.41653.5805-6.158237.694278.5391
26.7998-0.5312-0.89717.25532.13137.9808-0.5045-0.91240.99560.45152.67811.9683-0.46941.6477-1.74361.00390.15210.49951.22020.10491.8675-9.39640.340484.6674
32.3809-0.3965-1.10678.552-1.8227.20261.2377-0.09390.98561.1806-1.675-1.9808-1.0945-0.2962-0.82671.7621-0.3853-0.3411.4860.25511.7029-14.919135.531292.4916
40.60651.1981.12182.23452.26742.44692.66410.5027-2.65580.59650.8722-0.38560.12550.4225-1.99812.1138-0.42550.18832.8038-0.25673.2745-12.627332.852791.6884
53.8864-2.38550.33377.4566-3.17071.50951.2239-2.70950.90092.1092.4435-0.2311-0.37061.033-1.22341.07840.4918-0.04862.56690.15711.6539-12.052751.446695.408
65.9791.74842.480.48970.70852.636-0.51671.7812-1.07590.35220.42832.34451.2592-1.5723-0.92042.1963-0.65180.53112.17370.14842.26120.237628.014887.247
79.5051.22280.16134.482-1.02453.32930.5487-1.45531.84980.6129-1.0481.5711-1.21791.2190.08980.9531-0.4149-0.33832.3227-0.37882.7605-0.201927.6136102.0366
83.4038-0.73872.67790.8407-1.15762.2489-1.18480.81660.60010.1273-1.2751-0.5648-0.01780.879-3.32561.88180.8498-2.18742.04070.75943.249910.031625.245100.6065
94.99620.0332.57417.055-2.27073.53010.2999-0.6481-0.44040.72140.9174-0.04232.35860.0827-0.69492.22410.5318-0.15362.33380.37691.546.048224.996896.6431
100.60090.3492-0.37840.27270.37454.0144-0.33460.1307-1.23770.4017-0.10090.4016-0.39540.63810.06940.69670.0560.12031.60930.63413.073232.179629.500912.5065
113.96692.971-0.93147.94930.47596.9336-2.00130.6562-1.70870.85662.1393-0.36850.45650.8864-0.32391.81610.91360.2461.8142-0.10552.115130.301521.429715.8184
124.51673.7053.46533.77254.94097.09630.11192.5249-2.78960.65541.5564-3.3285-0.82911.8938-2.42512.56310.2263-0.43521.6123-0.35261.902531.982928.233320.7646
137.40955.0558-0.59613.5172-0.04768.1224-0.14831.9482-0.3616-0.01141.7767-2.39831.3017-1.817-1.01652.069-0.0110.19881.04940.24682.111323.601328.286813.9422
143.7129-2.7055-2.95372.37731.94943.11980.29621.538-1.1996-1.17130.2575-0.5627-0.0482-1.396-0.29792.0345-0.0374-0.29072.3304-0.01571.745524.755929.958627.5611
156.1817-1.8747-1.92763.2304-1.77662.4338-0.7762-0.84130.29790.3717-0.0668-0.995-0.3675-1.03180.1951.7729-0.0069-0.28551.41230.11541.289631.000623.85525.5818
160.5816-0.2792-1.2640.22240.89233.22921.61370.0788-0.5587-0.09180.30343.00670.33510.9602-1.18262.2612-0.1372-0.08091.93170.66972.411122.513314.111536.2222
171.01391.4808-1.50124.8916-1.99236.5171-1.16980.39990.9760.80680.33050.0480.2935-1.6192-0.15843.30191.3986-0.42372.50170.67742.251727.00585.132633.7864
188.07625.6955-8.2539.2338-6.83019.13760.8828-0.6089-2.2469-0.81420.49132.13042.2621-1.6733-0.69031.6309-0.2747-0.78683.9439-0.12652.552323.44941.538530.2553
196.28542.5994-2.55563.6131-1.28482.80890.27522.8762-1.6108-2.3229-0.05490.6954-0.5252-1.0377-0.56412.46221.3028-0.84553.1713-0.14081.616726.43567.658830.6895
207.91375.8945-1.16458.6381.21267.78680.5889-0.2402-0.33010.6278-0.3174-0.64250.1528-0.177-0.16630.99950.1438-0.25932.2102-0.14091.13729.376528.9947-4.3695
216.0899-0.87062.97143.424-1.17041.3486-1.2696-0.4825-1.33870.38241.11750.538-0.1141-0.7447-0.26171.7522-0.07530.24652.2847-0.07641.386916.571832.7568-16.4447
225.2771.96450.37174.4280.23788.89160.1944-1.03590.88330.29721.1123-1.97440.35710.8906-1.36061.230.338-0.09272.0042-0.92061.9524-13.838140.208265.3983
233.2461-0.8031-0.22054.5302-0.39631.7656-0.4093-0.18171.2492-1.90340.8402-1.44660.8337-0.29230.30140.7655-0.38560.62982.47060.55262.4972-9.775941.620258.918
240.51981.71380.19425.8878-2.27786.6201-0.0382-0.95520.4876-1.26630.0349-0.4481.29170.8598-0.14811.15590.2817-0.05082.2731-0.6081.7454-11.904438.377453.9213
252.4436-1.0199-0.40579.81355.20384.1416-0.42080.6169-1.61160.19190.08430.86451.6914-0.495-0.16782.3444-0.1552-0.20581.2257-0.10422.2998-23.866722.828347.1854
264.7218-0.6521-3.17227.37342.9892.97790.9095-0.24290.5251-0.7525-0.33340.03752.0985-0.10861.05942.53320.7657-0.14542.0041-0.04051.5206-24.522231.955145.5231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 69 )A45 - 69
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 124 )A70 - 124
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 147 )A125 - 147
4X-RAY DIFFRACTION4chain 'A' and (resid 148 through 158 )A148 - 158
5X-RAY DIFFRACTION5chain 'A' and (resid 159 through 178 )A159 - 178
6X-RAY DIFFRACTION6chain 'A' and (resid 179 through 204 )A179 - 204
7X-RAY DIFFRACTION7chain 'A' and (resid 205 through 233 )A205 - 233
8X-RAY DIFFRACTION8chain 'A' and (resid 234 through 257 )A234 - 257
9X-RAY DIFFRACTION9chain 'A' and (resid 258 through 311 )A258 - 311
10X-RAY DIFFRACTION10chain 'B' and (resid 47 through 60 )B47 - 60
11X-RAY DIFFRACTION11chain 'B' and (resid 61 through 83 )B61 - 83
12X-RAY DIFFRACTION12chain 'B' and (resid 84 through 107 )B84 - 107
13X-RAY DIFFRACTION13chain 'B' and (resid 108 through 123 )B108 - 123
14X-RAY DIFFRACTION14chain 'B' and (resid 124 through 162 )B124 - 162
15X-RAY DIFFRACTION15chain 'B' and (resid 163 through 208 )B163 - 208
16X-RAY DIFFRACTION16chain 'B' and (resid 209 through 233 )B209 - 233
17X-RAY DIFFRACTION17chain 'B' and (resid 234 through 257 )B234 - 257
18X-RAY DIFFRACTION18chain 'B' and (resid 258 through 271 )B258 - 271
19X-RAY DIFFRACTION19chain 'B' and (resid 272 through 307 )B272 - 307
20X-RAY DIFFRACTION20chain 'C' and (resid 45 through 147 )C45 - 147
21X-RAY DIFFRACTION21chain 'C' and (resid 148 through 308 )C148 - 308
22X-RAY DIFFRACTION22chain 'D' and (resid 45 through 83 )D45 - 83
23X-RAY DIFFRACTION23chain 'D' and (resid 84 through 133 )D84 - 133
24X-RAY DIFFRACTION24chain 'D' and (resid 134 through 212 )D134 - 212
25X-RAY DIFFRACTION25chain 'D' and (resid 213 through 282 )D213 - 282
26X-RAY DIFFRACTION26chain 'D' and (resid 283 through 308 )D283 - 308

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