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- EMDB-4198: Localized reconstruction of the Rift Valley fever virus glycoprot... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4198 | |||||||||
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Title | Localized reconstruction of the Rift Valley fever virus glycoprotein hexamer type 1 | |||||||||
![]() | Localized Reconstruction of Rift Valley fever virus type 1 hexamer | |||||||||
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![]() | enveloped virus / RVFV / glycoprotein / fusion protein / VIRUS | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||
![]() | Halldorsson S / Huiskonen JT | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.7 KB 12.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 4.7 KB | Display | ![]() |
Images | ![]() | 131.3 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6f9cMC ![]() 4197C ![]() 4199C ![]() 4200C ![]() 4201C ![]() 4202C ![]() 4203C ![]() 4204C ![]() 4205C ![]() 4206C ![]() 4207C ![]() 4208C ![]() 4209C ![]() 4210C ![]() 4211C ![]() 6f8pC ![]() 6f9bC ![]() 6f9dC ![]() 6f9eC ![]() 6f9fC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Localized Reconstruction of Rift Valley fever virus type 1 hexamer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Rift Valley fever virus
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Rift Valley fever virus
Supramolecule | Name: 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 |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Name: Glycoprotein shell / Diameter: 1100.0 Å / T number (triangulation number): 12 |
-Macromolecule #1: Glycoprotein
Macromolecule | Name: Glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 34.968902 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 UniProtKB: Envelopment polyprotein |
-Macromolecule #2: Glycoprotein
Macromolecule | Name: Glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 46.85557 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 UniProtKB: Envelopment polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 / Details: PBS |
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Vitrification | Cryogen name: ETHANE-PROPANE |
Details | Fixed with 0.2% v/v formaldehyde in PBS |
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Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 22.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-6f9c: |