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Basic information

Entry
Database: EMDB / ID: EMD-1015
TitleCryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus.
Map dataSemliki Forest virus.
Sample
  • Sample: Semliki Forest Virus
  • Virus: Semliki forest virus
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont entry into host cell / viral translational frameshifting ...togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont entry into host cell / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / identical protein 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
Similarity search - Component
Biological speciesSemliki forest virus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsMancini EJ / Clarke M / Gowen B / Rutten T / Fuller SD
CitationJournal: Mol Cell / Year: 2000
Title: Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus.
Authors: E J Mancini / M Clarke / B E Gowen / T Rutten / S D Fuller /
Abstract: Semliki Forest virus serves as a paradigm for membrane fusion and assembly. Our icosahedral reconstruction combined 5276 particle images from 48 cryo-electron micrographs and determined the virion ...Semliki Forest virus serves as a paradigm for membrane fusion and assembly. Our icosahedral reconstruction combined 5276 particle images from 48 cryo-electron micrographs and determined the virion structure to 9 A resolution. The improved resolution of this map reveals an N-terminal arm linking capsid subunits and defines the spike-capsid interaction sites. It illustrates the paired helical nature of the transmembrane segments and the elongated structures connecting them to the spike projecting domains. A 10 A diameter density in the fusion protein lines the cavity at the center of the spike. These clearly visible features combine with the variation in order between the layers to provide a framework for understanding the structural changes during the life cycle of an enveloped virus.
History
DepositionOct 10, 2002-
Header (metadata) releaseOct 11, 2002-
Map releaseOct 11, 2002-
UpdateJun 29, 2016-
Current statusJun 29, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4000
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4000
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1dyl
  • Surface level: 4000
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2xfc
  • Surface level: 4000
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1dyl
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2xfc
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1015.gif

Downloads & links

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Map

FileDownload / File: emd_1015.map.gz / Format: CCP4 / Size: 50.8 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationSemliki Forest virus.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.52 Å/pix.
x 301 pix.
= 758.52 Å		2.52 Å/pix.
x 301 pix.
= 758.52 Å		2.52 Å/pix.
x 301 pix.
= 758.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.52 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 9460.0 / Movie #1: 4000
Minimum - Maximum-25432.0 - 25955.0
Average (Standard dev.)-39.429400000000001 (±4659.710000000000036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-149-149-149
Dimensions301301301
Spacing301301301
CellA=B=C: 758.52 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z2.522.522.52
M x/y/z301301301
origin x/y/z0.0000.0000.000
length x/y/z758.520758.520758.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-149-149-149
NC/NR/NS301301301
D min/max/mean-25432.00025955.000-39.429

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Supplemental data

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Supplemental map: emd 1015 additional 1.map

Fileemd_1015_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 1015 additional 2.map

Fileemd_1015_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 1015 additional 3.map

Fileemd_1015_additional_3.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 : Semliki Forest Virus

EntireName: Semliki Forest Virus
Components
  • Sample: Semliki Forest Virus
  • Virus: Semliki forest virus

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Supramolecule #1000: Semliki Forest Virus

SupramoleculeName: Semliki Forest Virus / type: sample / ID: 1000 / Oligomeric state: T=4 membraneous particle / Number unique components: 1
Molecular weightTheoretical: 50 MDa / Method: theoretical

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Supramolecule #1: Semliki forest virus

SupramoleculeName: Semliki forest virus / type: virus / ID: 1 / Name.synonym: SFV / NCBI-ID: 11033 / Sci species name: Semliki forest virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: SFV
Host (natural)Organism: baby hamster kidney 21 cells (unknown) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: envelope / T number (triangulation number): 4
Virus shellShell ID: 2 / Name: nucleocapsid / T number (triangulation number): 4

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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

Concentration3 mg/mL
BufferpH: 7.4 / Details: Tris (10mM) NaCl (100 mM) ph 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 37 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: EMBL plunger with warm humid air spray. plunging at ambient temperature and humidity
Method: Blot for 2 sec Graticule grids were used to maintain flatness

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/ST
TemperatureAverage: 105 K
DateJan 1, 1995
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 48 / Average electron dose: 8 e/Å2 / Camera length: 44 / Od range: 1 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 7.628 µm / Nominal defocus min: 0.975 µm / Nominal magnification: 50000
Sample stageSpecimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: ctf multiplication and summation of normalized reconstructions
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: EMBL-ICOS
Details: final maps were calculated by making a normalized sum of seperate ctf multiplied maps: Baker, T. S., Olson, N. H., and Fuller, S. D. (1999). Adding the third dimension to virus life cycles: ...Details: final maps were calculated by making a normalized sum of seperate ctf multiplied maps: Baker, T. S., Olson, N. H., and Fuller, S. D. (1999). Adding the third dimension to virus life cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs. Microbiology and Molecular Biology Reviews 63, 862-922. Fuller, S. D., Butcher, S. J., Cheng, R. H., and Baker, T. S. (1996). Three-dimensional reconstruction of icosahedral particles-the uncommon line. J Struct Biol 116, 48-55. Mancini, E. J., Clarke, M., Gowen, B., Rutten, T., and Fuller, S. D. (2000). Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus. Molecular Cell 5, 255-266. Mancini, E. J., de Haas, F., and Fuller, S. D. (1997). High-resolution icosahedral reconstruction: fulfilling the promise of cryo-electron microscopy. Structure 5, 741-750.
Number images used: 6000
Final angle assignmentDetails: sufficient to give maximum inverse eigenvalue of 0.1

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Atomic model buiding 1

Initial modelPDB ID:

1dyl


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D
SoftwareName: emfit (Cheng et al 1995)
DetailsProtocol: rigid body. The capsid protein used for the rigid body refinement was PDB entry 1VCQ
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: R factor and clashes
Output model

PDB-1dyl:
9 ANGSTROM RESOLUTION CRYO-EM RECONSTRUCTION STRUCTURE OF SEMLIKI FOREST VIRUS (SFV) AND FITTING OF THE CAPSID PROTEIN STRUCTURE IN THE EM DENSITY

PDB-2xfc:
CHIKUNGUNYA E1 E2 ENVELOPE GLYCOPROTEINS FITTED IN SEMLIKI FOREST VIRUS cryo-EM MAP

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