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- EMDB-23378: CryoEM structure of Mayaro virus -

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Basic information

Entry
Database: EMDB / ID: EMD-23378
TitleCryoEM structure of Mayaro virus
Map dataCryoEM density map of MAYV focused region
Sample
  • Virus: Mayaro virus
    • Protein or peptide: Capsid protein
    • Protein or peptide: E1 protein
    • Protein or peptide: E2 protein
Keywordsalphavirus / togavirus / enveloped virus / pathogen / VIRAL PROTEIN
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein / Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesMayaro virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsChmielewski D / Kaelber J
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI120943 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P41GM103832 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 Allergy and Infectious Diseases (NIH/NIAID)R01AI153433 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R24AI120942 United States
CitationJournal: To Be Published
Title: Near-atomic resolution Cryo-EM structure of Mayaro virus identifies key structural determinants of alphavirus particle formation
Authors: Chmielewski D / Kaelber JT / Jin J / Weaver S / Auguste AJ / Chiu W
History
DepositionJan 27, 2021-
Header (metadata) releaseFeb 9, 2022-
Map releaseFeb 9, 2022-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.96
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.96
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7lih
  • Surface level: 3.96
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7lih
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23378.png

Downloads & links

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Map

FileDownload / File: emd_23378.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM density map of MAYV focused region
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: 3.96 / Movie #1: 3.96
Minimum - Maximum-20.100742 - 29.759705
Average (Standard dev.)0.01886207 (±0.7562586)
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 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2841.2841.284
M x/y/z720720720
origin x/y/z0.0000.0000.000
length x/y/z924.480924.480924.480
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ180180180
MAP C/R/S123
start NC/NR/NS-360-360-360
NC/NR/NS720720720
D min/max/mean-20.10129.7600.019

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Supplemental data

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Additional map: CryoEM density map of MAYV virion

Fileemd_23378_additional_1.map
AnnotationCryoEM density map of MAYV virion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoEM density map of E1-E2-E3-CP subunit.

Fileemd_23378_additional_2.map
AnnotationCryoEM density map of E1-E2-E3-CP subunit.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mayaro virus

EntireName: Mayaro virus
Components
  • Virus: Mayaro virus
    • Protein or peptide: Capsid protein
    • Protein or peptide: E1 protein
    • Protein or peptide: E2 protein

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Supramolecule #1: Mayaro virus

SupramoleculeName: Mayaro virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 59301 / Sci species name: Mayaro virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Virus shellShell ID: 1 / Diameter: 700.0 Å / T number (triangulation number): 4

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mayaro virus
Molecular weightTheoretical: 17.596111 KDa
SequenceString:
RERMCMKIEH DCIFEVKHEG KVTGYACLVG DKVMKPAHVP GVIDNADLAR LSYKKSSKYD LECAQIPVAM KSDASKYTHE KPEGHYNWH YGAVQYTGGR FTVPTGVGKP GDSGRPIFDN KGPVVAIVLG GANEGTRTAL SVVTWNKDMV TKITPEGTVE W

UniProtKB: Structural polyprotein

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Macromolecule #2: E1 protein

MacromoleculeName: E1 protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mayaro virus
Molecular weightTheoretical: 47.182426 KDa
SequenceString: YEHTAVIPNQ VGFPYKAHVA REGYSPLTLQ MQVVETSLEP TLNLEYITCD YKTKVPSPYV KCCGTAECRT QDKPEYKCAV FTGVYPFMW GGAYCFCDSE NTQMSEAYVE RADVCKHDYA AAYRAHTASL RAKIKVTYGT VNQTVEAYVN GDHAVTLAGT K FIFGPVST ...String:
YEHTAVIPNQ VGFPYKAHVA REGYSPLTLQ MQVVETSLEP TLNLEYITCD YKTKVPSPYV KCCGTAECRT QDKPEYKCAV FTGVYPFMW GGAYCFCDSE NTQMSEAYVE RADVCKHDYA AAYRAHTASL RAKIKVTYGT VNQTVEAYVN GDHAVTLAGT K FIFGPVST AWTPFDTKIV VYKGEVYNQD FPPYGAGQPG RFGDIQSRTL DSKDLYANTG LKLARPAAGN IHVPYTQTPS GF KTWQKDR DSPLNAKAPF GCTIQTNPVR AMNCAVGNIP VSMDIADSAF TRLTDAPIIS ELLCTVSTCT HSSDFGGVAV LSY KVEKAG RCDVHSHSNV AVLQEVSIEA EGRSVIHFST ASAAPSFIVS VCSSRATCTA KCEPPKDHVV TYPANHNGIT LPDL SSTAM TWAQHLAGGV GLLIALAVLI LVIVTCITLR

UniProtKB: Structural polyprotein

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Macromolecule #3: E2 protein

MacromoleculeName: E2 protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mayaro virus
Molecular weightTheoretical: 45.54491 KDa
SequenceString: NAYKLTRPYV AYCADCGMGH SCHSPAMIEN VQADATDGTL KIQFASQIGL TKTDTHDHTK IRYAEGHDIA EAARSTLKVH SSSECAVTG TMGHFILAKC PPGEVISVSF VDSKNEQRTC RIAYHHEQRL IGRERFTVRP HHGIELPCTT YQLTTAETSE E IDMHMPPD ...String:
NAYKLTRPYV AYCADCGMGH SCHSPAMIEN VQADATDGTL KIQFASQIGL TKTDTHDHTK IRYAEGHDIA EAARSTLKVH SSSECAVTG TMGHFILAKC PPGEVISVSF VDSKNEQRTC RIAYHHEQRL IGRERFTVRP HHGIELPCTT YQLTTAETSE E IDMHMPPD IPDRTILSQQ SGNVKITVNG RTVKYSCSCG SKPSGTTTTD KTINSCTVDK CQAYVTSHTK WQFNSPFVPR AE QAERKGK VHIPFPLINT TCRVPLAPEA LVRSGKREAT LSLHPIHPTL LSYRTLGREP VFDEQWITTQ TEVTIPVPVE GVE YRWGNH KPQRLWSQLT TEGRAHGWPH EIIEYYYGLH PTTTIVVVIR VSVVVLLSFA ASVYMCVVAR TKCLTPYALT PGAV VPVTI GVLCC

UniProtKB: Structural polyprotein

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 3200FSC
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD

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Image processing

Particle selectionNumber selected: 22314
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12219
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
Final angle assignmentType: PROJECTION MATCHING

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