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- EMDB-28780: Eilat virus/Eastern equine encephalitis virus chimeric vaccine ca... -

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Entry
Database: EMDB / ID: EMD-28780
TitleEilat virus/Eastern equine encephalitis virus chimeric vaccine candidate
Map dataT=4 common-lines map
SampleEilat virus/Eastern equine encephalitis virus chimeric virus != synthetic viruses

Eilat virus/Eastern equine encephalitis virus chimeric virus

  • Virus: synthetic viruses
    • Protein or peptide: EEEV nucleocapsid protein
    • Protein or peptide: EEEV glycoprotein E1
    • Protein or peptide: EEEV glycoprotein E2
    • Protein or peptide: EEEV glycoprotein E3
Keywordsalphavirus / togavirus / Togaviridae / EEEV / encephalitis / virus / virion / arbovirus
Biological speciesEastern equine encephalitis virus / synthetic viruses
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsKaelber JT / Chmielewski D / Chiu W / Auguste AJ
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI153433 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K22AI125474 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institute of Food and Agriculture (NIFA, United States)VA160103 United States
Robert A. Welch FoundationQ1242 United States
CitationJournal: Viruses / Year: 2022
Title: Alphavirus Particles Can Assemble with an Alternate Triangulation Number.
Authors: Jason T Kaelber / David Chmielewski / Wah Chiu / Albert J Auguste /
Abstract: Alphaviruses are spherical, enveloped RNA viruses primarily transmitted by mosquitoes, and cause significant arthritogenic and neurotropic disease in humans and livestock. Previous reports have shown ...Alphaviruses are spherical, enveloped RNA viruses primarily transmitted by mosquitoes, and cause significant arthritogenic and neurotropic disease in humans and livestock. Previous reports have shown that-in contrast to prototypical icosahedral viruses-alphaviruses incorporate frequent defects, and these may serve important functions in the viral life cycle. We confirm the genus-wide pleomorphism in live viral particles and extend our understanding of alphavirus assembly through the discovery of an alternate architecture of Eastern equine encephalitis virus (EEEV) particles. The alternate = 3 icosahedral architecture differs in triangulation number from the classic = 4 icosahedral organization that typifies alphaviruses, but the alternate architecture maintains the quasi-equivalence relationship of asymmetric units. The fusion spike glycoproteins are more loosely apposed in the = 3 form with corresponding changes in the underlying capsid protein lattice. This alternate architecture could potentially be exploited in engineering alphavirus-based particles for delivery of alphaviral or other RNA.
History
DepositionNov 3, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28780.png

Downloads & links

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Map

FileDownload / File: emd_28780.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT=4 common-lines map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.28 Å/pix.
x 720 pix.
= 924.48 Å		1.28 Å/pix.
x 720 pix.
= 924.48 Å		1.28 Å/pix.
x 720 pix.
= 924.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.284 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.5
Minimum - Maximum-16.466887 - 21.05331
Average (Standard dev.)0.23730162 (±1.2553841)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-360-360-360
Dimensions720720720
Spacing720720720
CellA=B=C: 924.48004 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: T=3 sub-map

Fileemd_28780_additional_1.map
AnnotationT=3 sub-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: odd half-map, unmasked unfiltered

Fileemd_28780_half_map_1.map
Annotationodd half-map, unmasked unfiltered
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: even half-map, unmasked unfiltered

Fileemd_28780_half_map_2.map
Annotationeven half-map, unmasked unfiltered
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Eilat virus/Eastern equine encephalitis virus chimeric virus

EntireName: Eilat virus/Eastern equine encephalitis virus chimeric virus
Components
  • Virus: synthetic viruses
    • Protein or peptide: EEEV nucleocapsid protein
    • Protein or peptide: EEEV glycoprotein E1
    • Protein or peptide: EEEV glycoprotein E2
    • Protein or peptide: EEEV glycoprotein E3

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Supramolecule #1: synthetic viruses

SupramoleculeName: synthetic viruses / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Viral genome contains EEEV-FL 93-939 structural proteins and Eilat virus nonstructural proteins. Chimeric virus described in "Novel Insect-Specific Eilat Virus-Based Chimeric Vaccine ...Details: Viral genome contains EEEV-FL 93-939 structural proteins and Eilat virus nonstructural proteins. Chimeric virus described in "Novel Insect-Specific Eilat Virus-Based Chimeric Vaccine Candidates Provide Durable, Mono- and Multivalent, Single-Dose Protection against Lethal Alphavirus Challenge" by Erasmus et al.
NCBI-ID: 512285 / Sci species name: synthetic viruses / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / T number (triangulation number): 4

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Macromolecule #1: EEEV nucleocapsid protein

MacromoleculeName: EEEV nucleocapsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO / EC number: togavirin
Source (natural)Organism: Eastern equine encephalitis virus / Strain: FL93-939
SequenceString:
CMKLESDKTF PIMLNGQVNG YACVVGGRMF KPLHVEGRID NEQLAAIKLK KASIYDLEYG DVPQCMKSDT LQYTSDKPP GFYNWHHGAV QYENNRFTVP RGVGGKGDSG RPILDNKGRV VAIVLGGVNE GSRTALSVVT W NQKGVTVK DTPEGSEPW

GENBANK: GENBANK: AAF04796.1

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Macromolecule #2: EEEV glycoprotein E1

MacromoleculeName: EEEV glycoprotein E1 / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO / EC number: togavirin
Source (natural)Organism: Eastern equine encephalitis virus / Strain: FL93-939
SequenceString: KADDTLQVLN YLWNNNQNFF WMQTLIPLAA LIVSMRMLRC LFCCGPAFLL VCGALGAAAY EHTAVMPNKV GIPYKALVE RPGYAPVHLQ IQLVNTRIIP STNLEYITCK YKTKVPSPVV KCCGATQCSS KPHPDYQCQV F TGVYPFMW GGAYCFCDTE NTQMSEAYVE ...String:
KADDTLQVLN YLWNNNQNFF WMQTLIPLAA LIVSMRMLRC LFCCGPAFLL VCGALGAAAY EHTAVMPNKV GIPYKALVE RPGYAPVHLQ IQLVNTRIIP STNLEYITCK YKTKVPSPVV KCCGATQCSS KPHPDYQCQV F TGVYPFMW GGAYCFCDTE NTQMSEAYVE RSEECSIDHA KAYKVHTGTV QAMVNITYGS VSWRSADVYV NG ETPAKIG DAKLIIGPLS SAWSPFDNKV VVYGHEVYNY DFPEYGTGKA GSFGDLQSRT STSNDLYANT NLK LQRPQA GIVHTPFTQA PSGFERWKRD KGAPLNDVAP FGCSIALEPL RAENCAVGSI PISIDIPDAA FTRI SETPT VSDLECKITE CTYASDFGGI ATVAYKSSKA GNCPIHSPSG VAVIKENDVT LAESGSFTFH FSTAN IHPA FKLQVCTSAV TCKGDCKPPK DHIVDYPAQH TDLLTSAISA TAWSWLKVLV GGTSAFIVLG LIATAV VAL VLF

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Macromolecule #3: EEEV glycoprotein E2

MacromoleculeName: EEEV glycoprotein E2 / type: protein_or_peptide / ID: 3 / Enantiomer: DEXTRO / EC number: togavirin
Source (natural)Organism: Eastern equine encephalitis virus
SequenceString: PYIADCPNCG HSRCDSPIAI EEVRGDAHAG AIRIQTSAMF GLKTDGVDLA YMSFMNGKTQ KSIKIDNLHV RTSAPCSLV SHHGYYILAQ CPPGDTVTVG FHDGPNRHTC TVAHKVEFRP VGREEYRHPP EHGVELPCNR Y THKRADQG HYVEMHQPGL VADHSLLSIH ...String:
PYIADCPNCG HSRCDSPIAI EEVRGDAHAG AIRIQTSAMF GLKTDGVDLA YMSFMNGKTQ KSIKIDNLHV RTSAPCSLV SHHGYYILAQ CPPGDTVTVG FHDGPNRHTC TVAHKVEFRP VGREEYRHPP EHGVELPCNR Y THKRADQG HYVEMHQPGL VADHSLLSIH SAKVKITVPS GAQVKYYCKC PDVREGITSS DHTTTCTDVK QC RAYLIDN KKWVYNFGRL LRGEGDTFKG KLHVPFVPVK AKCIATLAPE LLVEHKHRTL ILHLHPDHPT LLT TRSLGS DANPIRQWIE RPTTVNFTVT GEGLEYTWGN HPPKRVWAQE SGEGNPHGWP HEVVVYYYNR YPLT TIIGL CTCVAIIMVS CVTSVWLLCR ARNLCITPYK LAPNAQVPIL LALLCC

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Macromolecule #4: EEEV glycoprotein E3

MacromoleculeName: EEEV glycoprotein E3 / type: protein_or_peptide / ID: 4 / Enantiomer: DEXTRO / EC number: togavirin
Source (natural)Organism: Eastern equine encephalitis virus / Strain: FL93-939
SequenceString:
MCVLANITFP CDQPPCMPCC YEKNPHETLT MLEQNYDSRT YDQLLDAAVK CNARRTRR

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
0.1 MNaClsodium chloride
0.001 MC10H16N2O8Ethylenediaminetetraacetic acid
0.05 MC4H11NO3tris(hydroxymethyl)aminomethane

Details: "TEN buffer": 0.05 M Tris-HCl [pH 7.4], 0.1 M NaCl, 0.001 M EDTA
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureMin: 86.8 K
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 4 / Number real images: 2068 / Average exposure time: 6.0 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 30000
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: NONE / Details: common lines
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: MPSA / Details: 5 iterations MPSA / Number images used: 23332
Initial angle assignmentType: COMMON LINE / Software - Name: MPSA
Final angle assignmentType: COMMON LINE / Software - Name: MPSA
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 1)
FSC plot (resolution estimation)

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