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- EMDB-9693: Cryo-EM structure of an alphavirus, Sindbis virus -

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Basic information

Entry
Database: EMDB / ID: EMD-9693
TitleCryo-EM structure of an alphavirus, Sindbis virus
Map dataCryo-EM structure of an alphavirus, Sindbis virus
Sample
  • Virus: Sindbis virus
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Assembly protein E3
  • Ligand: Octadecane
KeywordsAlphavirus / Sindbis virus / Glycoprotein / VIRUS
Function / homology
Function and homology information


viral capsid / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis ...viral capsid / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / plasma membrane / cytoplasm
Similarity search - Function
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 ...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 speciesSindbis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang X / Ma J
CitationJournal: Nat Commun / Year: 2018
Title: Implication for alphavirus host-cell entry and assembly indicated by a 3.5Å resolution cryo-EM structure.
Authors: Lihong Chen / Ming Wang / Dongjie Zhu / Zhenzhao Sun / Jun Ma / Jinglin Wang / Lingfei Kong / Shida Wang / Zaisi Liu / Lili Wei / Yuwen He / Jingfei Wang / Xinzheng Zhang /
Abstract: Alphaviruses are enveloped RNA viruses that contain several human pathogens. Due to intrinsic heterogeneity of alphavirus particles, a high resolution structure of the virion is currently lacking. ...Alphaviruses are enveloped RNA viruses that contain several human pathogens. Due to intrinsic heterogeneity of alphavirus particles, a high resolution structure of the virion is currently lacking. Here we provide a 3.5 Å cryo-EM structure of Sindbis virus, using block based reconstruction method that overcomes the heterogeneity problem. Our structural analysis identifies a number of conserved residues that play pivotal roles in the virus life cycle. We identify a hydrophobic pocket in the subdomain D of E2 protein that is stabilized by an unknown pocket factor near the viral membrane. Residues in the pocket are conserved in different alphaviruses. The pocket strengthens the interactions of the E1/E2 heterodimer and may facilitate virus assembly. Our study provides structural insights into alphaviruses that may inform the design of drugs and vaccines.
History
DepositionOct 23, 2018-
Header (metadata) releaseMar 13, 2019-
Map releaseMar 13, 2019-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6imm
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6imm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9693.png

Downloads & links

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Map

FileDownload / File: emd_9693.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of an alphavirus, Sindbis virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 580 pix.
= 788.8 Å		1.36 Å/pix.
x 580 pix.
= 788.8 Å		1.36 Å/pix.
x 580 pix.
= 788.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-18.341950000000001 - 26.221699999999998
Average (Standard dev.)0.0027487886 (±0.9999224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-290-290-290
Dimensions580580580
Spacing580580580
CellA=B=C: 788.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z580580580
origin x/y/z0.0000.0000.000
length x/y/z788.800788.800788.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-290-290-290
NC/NR/NS580580580
D min/max/mean-18.34226.2220.003

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Supplemental data

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Sample components

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Entire : Sindbis virus

EntireName: Sindbis virus
Components
  • Virus: Sindbis virus
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Assembly protein E3
  • Ligand: Octadecane

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Supramolecule #1: Sindbis virus

SupramoleculeName: Sindbis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 11034 / Sci species name: Sindbis virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sindbis virus
Molecular weightTheoretical: 47.186434 KDa
SequenceString: FEHATTVPNV PRIPYKALVE RAGYAPLNLE ITVMSSELIP STNLEYVTCK YTTVVPSPKV KCCGTLECSS ARHADYNCKV FGGVYPFMW GGAQCFCDSE NSQMSEAYVE FSADCAADHA QAVKVHTAAL KAGLRIVYGN TTSMLDVYVN GVTPGTSKDL K VIAGPISA ...String:
FEHATTVPNV PRIPYKALVE RAGYAPLNLE ITVMSSELIP STNLEYVTCK YTTVVPSPKV KCCGTLECSS ARHADYNCKV FGGVYPFMW GGAQCFCDSE NSQMSEAYVE FSADCAADHA QAVKVHTAAL KAGLRIVYGN TTSMLDVYVN GVTPGTSKDL K VIAGPISA AYTPFDHKVI IHKGKVYNYD FPEYGAMKPG AFGDIQATSL TSNDLIANTD IRLLKPSAKN VHVPYTQAAS GF EMWKNNS GRPLQETAPF GCQIAVNPLR AVDCAYGNIP ISLDIPNAAF VRVSDAPLVT ALKCEVGECV YSADFGGIAT LQY SSDREG QCSVHSHSST ATLQESTVHV LQKGGATIHF STASPQANFI VSLCGKKTTC NAECKPPADH IVNVPHKNDQ EFQA AVSQT SWSWLFALFG GASSLLVIGV MIFACSALLT STRR

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Macromolecule #2: Spike glycoprotein E2

MacromoleculeName: Spike glycoprotein E2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sindbis virus
Molecular weightTheoretical: 43.184387 KDa
SequenceString: FTLTSPYLGT CSYCHHTEPC FSPVKIEQVW DEADDNTIRI QTSAQFGYDQ SGAASVNKYR IMSLKQDHTI EEGSMDAIKI STSGPCRRL NHKGYFLLAK CPPGDSVTVS ISAGDSATSC TLARKVKPKF VGREKYDLPP VHGKKIPCYI YDRLKETSAG Y ITMHRPGP ...String:
FTLTSPYLGT CSYCHHTEPC FSPVKIEQVW DEADDNTIRI QTSAQFGYDQ SGAASVNKYR IMSLKQDHTI EEGSMDAIKI STSGPCRRL NHKGYFLLAK CPPGDSVTVS ISAGDSATSC TLARKVKPKF VGREKYDLPP VHGKKIPCYI YDRLKETSAG Y ITMHRPGP HAYATYLEES SGKVYAKPPS GKNITYKSDQ TKWVFNSPDL IRHADHTAQG KMHLPFKLVP STCLVPLAHV PQ VVHGFKH ISLQLDTDHL TLLTTRRLGE KPEPTSEWII GKTVRNFSVG RDGFEYIWGN HEPVRVWAQE SAPGDPHGWP HEI VQHYYH RHPVYTVMIL VAATLAIVLG VSVASVCVCR ARRECLTPYA LAPNAVVPTS IALLCCIRPT SA

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Macromolecule #3: Assembly protein E3

MacromoleculeName: Assembly protein E3 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sindbis virus
Molecular weightTheoretical: 7.480542 KDa
SequenceString:
SAAPLVAAMC ILGNMTFPCN QPPTCYSREP ARALDILEAN VDSAAYDDLM RAVLRCTPSS RAKRNITDD

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Macromolecule #4: Octadecane

MacromoleculeName: Octadecane / type: ligand / ID: 4 / Number of copies: 1 / Formula: 8K6
Molecular weightTheoretical: 254.494 Da
Chemical component information

ChemComp-8K6:
Octadecane

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29974
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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