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- EMDB-4197: Icosahedral reconstruction of Rift Valley fever virus virion -

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Basic information

Entry
Database: EMDB / ID: EMD-4197
TitleIcosahedral reconstruction of Rift Valley fever virus virion
Map dataIcosahedral average of Rift Valley fever virus
Sample
  • Virus: Rift Valley fever virus
    • Protein or peptide: Glycoprotein
    • Protein or peptide: Glycoprotein
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host apoptosis / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Phlebovirus nonstructural NS-M / M polyprotein precursor, phlebovirus / Phlebovirus nonstructural protein NS-M / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain
Similarity search - Domain/homology
Envelopment polyprotein / Envelopment polyprotein / Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesRift valley fever virus / Rift Valley fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 13.3 Å
AuthorsHalldorsson S / Huiskonen JT
CitationJournal: Nat Commun / Year: 2018
Title: Shielding and activation of a viral membrane fusion protein.
Authors: Steinar Halldorsson / Sai Li / Mengqiu Li / Karl Harlos / Thomas A Bowden / Juha T Huiskonen /
Abstract: Entry of enveloped viruses relies on insertion of hydrophobic residues of the viral fusion protein into the host cell membrane. However, the intermediate conformations during fusion remain unknown. ...Entry of enveloped viruses relies on insertion of hydrophobic residues of the viral fusion protein into the host cell membrane. However, the intermediate conformations during fusion remain unknown. Here, we address the fusion mechanism of Rift Valley fever virus. We determine the crystal structure of the Gn glycoprotein and fit it with the Gc fusion protein into cryo-electron microscopy reconstructions of the virion. Our analysis reveals how the Gn shields the hydrophobic fusion loops of the Gc, preventing premature fusion. Electron cryotomography of virions interacting with membranes under acidic conditions reveals how the fusogenic Gc is activated upon removal of the Gn shield. Repositioning of the Gn allows extension of Gc and insertion of fusion loops in the outer leaflet of the target membrane. These data show early structural transitions that enveloped viruses undergo during host cell entry and indicate that analogous shielding mechanisms are utilized across diverse virus families.
History
DepositionDec 14, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseJan 31, 2018-
UpdateFeb 7, 2018-
Current statusFeb 7, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6f9b
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6f9b
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4197.png

Downloads & links

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Map

FileDownload / File: emd_4197.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral average of Rift Valley fever virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.7 Å/pix.
x 512 pix.
= 1382.4 Å		2.7 Å/pix.
x 512 pix.
= 1382.4 Å		2.7 Å/pix.
x 512 pix.
= 1382.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.01975869 - 0.06778468
Average (Standard dev.)0.0014033737 (±0.012627241)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 1382.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z1382.4001382.4001382.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0200.0680.001

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Supplemental data

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Sample components

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Entire : Rift Valley fever virus

EntireName: Rift Valley fever virus
Components
  • Virus: Rift Valley fever virus
    • Protein or peptide: Glycoprotein
    • Protein or peptide: Glycoprotein

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Supramolecule #1: Rift Valley fever virus

SupramoleculeName: Rift Valley fever virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Cultured in Vero cells / NCBI-ID: 11588 / Sci species name: Rift Valley fever virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Glycoprotein shell / Diameter: 1100.0 Å / T number (triangulation number): 12

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Macromolecule #1: Glycoprotein

MacromoleculeName: Glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Rift valley fever virus
Molecular weightTheoretical: 34.968902 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EDPHLRNRPG KGHNYIDGMT QEDATCKPVT YAGACSSFDV LLEKGKFPLF QSYAHHRTLL EAVHDTIIAK ADPPSCDLQS AHGNPCMKE KLVMKTHCPN DYQSAHYLNN DGKMASVKCP PKYELTEDCN FCRQMTGASL KKGSYPLQDL FCQSSEDDGS K LKTKMKGV ...String:
EDPHLRNRPG KGHNYIDGMT QEDATCKPVT YAGACSSFDV LLEKGKFPLF QSYAHHRTLL EAVHDTIIAK ADPPSCDLQS AHGNPCMKE KLVMKTHCPN DYQSAHYLNN DGKMASVKCP PKYELTEDCN FCRQMTGASL KKGSYPLQDL FCQSSEDDGS K LKTKMKGV CEVGVQALKK CDGQLSTAHE VVPFAVFKNS KKVYLDKLDL KTEENLLPDS FVCFEHKGQY KGKLDSGQTK RE LKSFDIS QCPKIGGHGS KKCTGDAAFC SAYECTAQYA NAYCSHANGS GIVQIQVSGV WKKPLCVGYE RVVVKRELS

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Macromolecule #2: Glycoprotein

MacromoleculeName: Glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Rift valley fever virus
Molecular weightTheoretical: 46.85557 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DPGCSELIQA SSRITTCSTE GVNTKCRLSG TALIRAGSVG AEACLMLKGV KEDQTKFLKI KTVSSELSCR EGQSYWTGSF SPKCLSSRR CHLVGECHVN RCLSWRDNET SAEFSFVGES TTMRENKCFE QCGGWGCGCF NVNPSCLFVH TYLQSVRKEA L RVFNCIDW ...String:
DPGCSELIQA SSRITTCSTE GVNTKCRLSG TALIRAGSVG AEACLMLKGV KEDQTKFLKI KTVSSELSCR EGQSYWTGSF SPKCLSSRR CHLVGECHVN RCLSWRDNET SAEFSFVGES TTMRENKCFE QCGGWGCGCF NVNPSCLFVH TYLQSVRKEA L RVFNCIDW VHKLTLEITD FDGSVSTIDL GASSSRFTNW GSVSLSLDAE GISGSNSFSF IESPGKGYAI VDEPFSEIPR QG FLGEIRC NSESSVLSAH ESCLRAPNLI SYKPMIDQLE CTTNLIDPFV VFERGSLPQT RNDKTFAASK GNRGVQAFSK GSV QADLTL MFDNFEVDFV GAAVSCDAAF LNLTGCYSCN AGARVCLSIT STGTGSLSAH NKDGSLHIVL PSENGTKDQC QILH FTVPE VEEEFMYSCD GDERPLLVKG TLIAID

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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: 7.5 / Details: PBS
VitrificationCryogen name: ETHANE-PROPANE
DetailsFixed with 0.2% v/v formaldehyde in PBS

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Electron microscopy

MicroscopeFEI TECNAI F30
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-88 / Average exposure time: 17.6 sec. / Average electron dose: 22.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4336
CTF correctionSoftware:
Namedetails
CTFFINDDetermination
RELIONCorrection
Startup modelType of model: EMDB MAP
EMDB ID:

1550

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 13.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 2995
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-6f9b:
Asymmetric unit of Rift Valley fever virus glycoprotein shell

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