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

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Basic information

Entry
Database: EMDB / ID: 9693
TitleCryo-EM structure of an alphavirus, Sindbis virus
Map dataCryo-EM structure of an alphavirus, Sindbis virus
SampleSindbis virus:
virus / (Spike glycoprotein ...) x 2 / Assembly protein E3 / ligand
SourceSindbis virus / SINV (virus)
Methodsingle particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsZhang X / Ma J / Chen L
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
Validation ReportPDB-ID: 6imm

SummaryFull reportAbout validation report
DateDeposition: Oct 23, 2018 / Header (metadata) release: Mar 13, 2019 / Map release: Mar 13, 2019 / Last update: Mar 13, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • 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 models: PDB-6imm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9693.map.gz (map file in CCP4 format, 780449 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
580 pix
1.36 Å/pix.
= 788.8 Å
580 pix
1.36 Å/pix.
= 788.8 Å
580 pix
1.36 Å/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
Contour Level:4.0 (by author), 4 (movie #1):
Minimum - Maximum-18.341950000000001 - 26.221699999999998
Average (Standard dev.)0.0027487886 (0.9999224)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions580580580
Origin-290.0-290.0-290.0
Limit289.0289.0289.0
Spacing580580580
CellA=B=C: 788.8 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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 / Number of components: 5

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Component #1: virus, Sindbis virus

VirusName: Sindbis virus / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Sindbis virus

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Component #2: protein, Spike glycoprotein E1

ProteinName: Spike glycoprotein E1 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 47.186434 kDa
SourceSpecies: SINV (virus)

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Component #3: protein, Spike glycoprotein E2

ProteinName: Spike glycoprotein E2 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 43.184387 kDa
SourceSpecies: SINV (virus)

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Component #4: protein, Assembly protein E3

ProteinName: Assembly protein E3 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 7.480542 kDa
SourceSpecies: SINV (virus)

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Component #5: ligand, Octadecane

LigandName: Octadecane / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.254494 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 29974
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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