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- EMDB-9281: CryoEM structure of chimeric Eastern Equine Encephalitis Virus: G... -

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Basic information

Entry
Database: EMDB / ID: EMD-9281
TitleCryoEM structure of chimeric Eastern Equine Encephalitis Virus: Genome-Binding Capsid N-terminal Domain
Map dataEEEV map low pass-filtered to 4.8A to visualize features of capsid N-terminal domain
Sample
  • Complex: Eastern equine encephalitis virus capsid
    • Protein or peptide: Capsid
KeywordsAlphavirus / EEEV / Eastern Equine Encephalitis Virus / Sindbis / VIRUS
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 / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane
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
Similarity search - Component
Biological speciesEastern equine encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsHasan SS / Sun C
Funding support United States, United Kingdom, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI095366 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2R01AI095436 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI117331-01 United States
Bill & Melinda Gates FoundationOPP1115782 United Kingdom
CitationJournal: Cell Rep / Year: 2018
Title: Cryo-EM Structures of Eastern Equine Encephalitis Virus Reveal Mechanisms of Virus Disassembly and Antibody Neutralization.
Authors: S Saif Hasan / Chengqun Sun / Arthur S Kim / Yasunori Watanabe / Chun-Liang Chen / Thomas Klose / Geeta Buda / Max Crispin / Michael S Diamond / William B Klimstra / Michael G Rossmann /
Abstract: Alphaviruses are enveloped pathogens that cause arthritis and encephalitis. Here, we report a 4.4-Å cryoelectron microscopy (cryo-EM) structure of eastern equine encephalitis virus (EEEV), an ...Alphaviruses are enveloped pathogens that cause arthritis and encephalitis. Here, we report a 4.4-Å cryoelectron microscopy (cryo-EM) structure of eastern equine encephalitis virus (EEEV), an alphavirus that causes fatal encephalitis in humans. Our analysis provides insights into viral entry into host cells. The envelope protein E2 showed a binding site for the cellular attachment factor heparan sulfate. The presence of a cryptic E2 glycan suggests how EEEV escapes surveillance by lectin-expressing myeloid lineage cells, which are sentinels of the immune system. A mechanism for nucleocapsid core release and disassembly upon viral entry was inferred based on pH changes and capsid dissociation from envelope proteins. The EEEV capsid structure showed a viral RNA genome binding site adjacent to a ribosome binding site for viral genome translation following genome release. Using five Fab-EEEV complexes derived from neutralizing antibodies, our investigation provides insights into EEEV host cell interactions and protective epitopes relevant to vaccine design.
History
DepositionOct 30, 2018-
Header (metadata) releaseDec 5, 2018-
Map releaseDec 19, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6mx7
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6mx7
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9281.png

Downloads & links

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Map

FileDownload / File: emd_9281.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEEEV map low pass-filtered to 4.8A to visualize features of capsid N-terminal domain
Voxel sizeX=Y=Z: 1.58 Å
Density
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-30.197924 - 51.027639999999998
Average (Standard dev.)0.13863319 (±3.4371722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-288-288-288
Dimensions576576576
Spacing576576576
CellA=B=C: 910.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.581.581.58
M x/y/z576576576
origin x/y/z0.0000.0000.000
length x/y/z910.080910.080910.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-288-288-288
NC/NR/NS576576576
D min/max/mean-30.19851.0280.139

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Supplemental data

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Half map: EEEV half map

Fileemd_9281_half_map_1.map
AnnotationEEEV half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EEEV half map

Fileemd_9281_half_map_2.map
AnnotationEEEV half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Eastern equine encephalitis virus capsid

EntireName: Eastern equine encephalitis virus capsid
Components
  • Complex: Eastern equine encephalitis virus capsid
    • Protein or peptide: Capsid

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Supramolecule #1: Eastern equine encephalitis virus capsid

SupramoleculeName: Eastern equine encephalitis virus capsid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purified from infected BHK-15 cells
Source (natural)Organism: Eastern equine encephalitis virus

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Macromolecule #1: Capsid

MacromoleculeName: Capsid / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Eastern equine encephalitis virus
Molecular weightTheoretical: 28.861496 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: MFPYPTLNYP PMAPINPMAY RDPNPPRQVA PFRPPLAAQI EDLRRSIANL TLKQRAPNPP AGPPAKRKKP APKPKPAQAK KKRPPPPAK KQKRKPKPGK RQRMCMKLES DKTFPIMLNG QVNGYACVVG GRVFKPLHVE GRIDNEQLAA IKLKKASIYD L EYGDVPQC ...String:
MFPYPTLNYP PMAPINPMAY RDPNPPRQVA PFRPPLAAQI EDLRRSIANL TLKQRAPNPP AGPPAKRKKP APKPKPAQAK KKRPPPPAK KQKRKPKPGK RQRMCMKLES DKTFPIMLNG QVNGYACVVG GRVFKPLHVE GRIDNEQLAA IKLKKASIYD L EYGDVPQC MKSDTLQYTS DKPPGFYNWH HGAVQYENNR FTVPRGVGGK GDSGRPILDN KGRVVAIVLG GVNEGSRTAL SV VTWNQKG VTVKDTPEGS EPW

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

Concentration1 mg/mL
BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: HELIUM / Chamber humidity: 80 % / Chamber temperature: 295 K / Instrument: GATAN CRYOPLUNGE 3

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 31.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30806
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6mx7:
CryoEM structure of chimeric Eastern Equine Encephalitis Virus: Genome-Binding Capsid N-terminal Domain

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