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- EMDB-22961: Cryo-EM structure of the mature and infective Mayaro virus -

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Entry
Database: EMDB / ID: EMD-22961
TitleCryo-EM structure of the mature and infective Mayaro virus
Map dataCryo-EM of the mature and infective Mayaro virus
Sample
  • Virus: Mayaro virus
Biological speciesMayaro virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsRibeiro Filho H / Coimbra LD / Cassago A / Rocha RFP / Padilha AC / Trivella DBB / Schatz M / Oliveira PSL / Portugal RV / Marques RE / van Heel M
Funding support Brazil, 3 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2017/15340-2 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)440379/2016-4 Brazil
Sao Paulo Research Foundation (FAPESP)2018/03917-6 Brazil
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM structure of the mature and infective Mayaro virus at 4.4 Å resolution reveals features of arthritogenic alphaviruses.
Authors: Helder V Ribeiro-Filho / Lais D Coimbra / Alexandre Cassago / Rebeca P F Rocha / João Victor da Silva Guerra / Rafael de Felicio / Carolina Moretto Carnieli / Luiza Leme / Antonio Cláudio ...Authors: Helder V Ribeiro-Filho / Lais D Coimbra / Alexandre Cassago / Rebeca P F Rocha / João Victor da Silva Guerra / Rafael de Felicio / Carolina Moretto Carnieli / Luiza Leme / Antonio Cláudio Padilha / Adriana F Paes Leme / Daniela B B Trivella / Rodrigo Villares Portugal / Paulo Sérgio Lopes-de-Oliveira / Rafael Elias Marques /
Abstract: Mayaro virus (MAYV) is an emerging arbovirus of the Americas that may cause a debilitating arthritogenic disease. The biology of MAYV is not fully understood and largely inferred from related ...Mayaro virus (MAYV) is an emerging arbovirus of the Americas that may cause a debilitating arthritogenic disease. The biology of MAYV is not fully understood and largely inferred from related arthritogenic alphaviruses. Here, we present the structure of MAYV at 4.4 Å resolution, obtained from a preparation of mature, infective virions. MAYV presents typical alphavirus features and organization. Interactions between viral proteins that lead to particle formation are described together with a hydrophobic pocket formed between E1 and E2 spike proteins and conformational epitopes specific of MAYV. We also describe MAYV glycosylation residues in E1 and E2 that may affect MXRA8 host receptor binding, and a molecular "handshake" between MAYV spikes formed by N262 glycosylation in adjacent E2 proteins. The structure of MAYV is suggestive of structural and functional complexity among alphaviruses, which may be targeted for specificity or antiviral activity.
History
DepositionNov 5, 2020-
Header (metadata) releaseApr 21, 2021-
Map releaseApr 21, 2021-
UpdateJun 9, 2021-
Current statusJun 9, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.9
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ko8
  • Surface level: 1.9
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ko8
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22961.png

Downloads & links

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Map

FileDownload / File: emd_22961.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of the mature and infective Mayaro virus
Voxel sizeX=Y=Z: 1.1074 Å
Density
Contour LevelBy AUTHOR: 1.9 / Movie #1: 1.9
Minimum - Maximum-7.5376306 - 9.131372
Average (Standard dev.)-3.04169e-05 (±0.55280685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 885.9199 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.10741.10741.1074
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z885.920885.920885.920
α/β/γ90.00090.00090.000
start NX/NY/NZ727265
NX/NY/NZ157157169
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS800800800
D min/max/mean-7.5389.131-0.000

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Supplemental data

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Sample components

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Entire : Mayaro virus

EntireName: Mayaro virus
Components
  • Virus: Mayaro virus

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Supramolecule #1: Mayaro virus

SupramoleculeName: Mayaro virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 59301 / Sci species name: Mayaro virus / Sci species strain: IQT4235 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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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

Concentration2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.0 mm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000
Specialist opticsSpherical aberration corrector: Cs corrrector used to minimise the spherical aberration
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 9100 / Average exposure time: 4.26 sec. / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 79000
CTF correctionSoftware - Name: IMAGIC (ver. 2019) / Software - details: Full data set CTF correction
Details: Per particle CTF correction based on IMAGIC movie spectra of all images simultaneously (Full data set CTF correction).
Startup modelType of model: OTHER / Details: Angular Reconstitution random startup
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC (ver. 2019)
Details: Angular reconstitution used originally in random startup mode, later in refinement mode using anchor sets
Final 3D classificationNumber classes: 30 / Avg.num./class: 1 / Software - Name: IMAGIC (ver. 2019)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC (ver. 2019)
Details: Angular reconstitution in refinement mode using anchor sets and local alignments
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 1/2 BIT CUT-OFF / Software - Name: IMAGIC (ver. 2019) / Software - details: with software extensions
Details: Random assignment of 3D membership to multiple 3D reconstructions during refinements, based on angular reconstitution.
Number images used: 40179

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