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- EMDB-33522: The pre-fusion structure of Thogotovirus dhori envelope glycoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-33522
TitleThe pre-fusion structure of Thogotovirus dhori envelope glycoprotein
Map data
Sample
  • Complex: Thogotovirus dhori envelope glycoprotein
    • Protein or peptide: Envelope glycoprotein
KeywordsViral surface protein / STRUCTURAL PROTEIN
Function / homologyBaculovirus Gp64, envelope glycoprotein / Baculovirus gp64 envelope glycoprotein / symbiont-mediated perturbation of host process / viral envelope / virion membrane / membrane / Envelope glycoprotein
Function and homology information
Biological speciesDhori thogotovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsShan YY / Zhang MF / Pei DQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2017YFA0504100 China
CitationJournal: To Be Published
Title: Pre- and post-fusion class III glycoprotein structures reveal viral fusion mechanism
Authors: Shan YY / Zhang MF / Pei DQ
History
DepositionJun 1, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33522.png

Downloads & links

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Map

FileDownload / File: emd_33522.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 480 pix.
= 407.52 Å		0.85 Å/pix.
x 480 pix.
= 407.52 Å		0.85 Å/pix.
x 480 pix.
= 407.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.849 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-0.6935368 - 1.2843701
Average (Standard dev.)0.00072422886 (±0.019427495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 407.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33522_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33522_half_map_2.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 : Thogotovirus dhori envelope glycoprotein

EntireName: Thogotovirus dhori envelope glycoprotein
Components
  • Complex: Thogotovirus dhori envelope glycoprotein
    • Protein or peptide: Envelope glycoprotein

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Supramolecule #1: Thogotovirus dhori envelope glycoprotein

SupramoleculeName: Thogotovirus dhori envelope glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Dhori thogotovirus

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Macromolecule #1: Envelope glycoprotein

MacromoleculeName: Envelope glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Dhori thogotovirus / Strain: Indian/1313/61
Molecular weightTheoretical: 58.674496 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDSTIRLVAT IFLISLTQQI EVCNKAQQQG PYTLVDYQEK PLNISRIQIK VVKTSVATKG LNFHIGYRAV WRSYCYNGGS LDKNTGCYN DLIPKSPTES ELRTWSKSQK CCTGPDAVDA WGSDARICWA EWKMELCHTA KELKKYSNNN HFAYHTCNLS W RCGLKSTH ...String:
MDSTIRLVAT IFLISLTQQI EVCNKAQQQG PYTLVDYQEK PLNISRIQIK VVKTSVATKG LNFHIGYRAV WRSYCYNGGS LDKNTGCYN DLIPKSPTES ELRTWSKSQK CCTGPDAVDA WGSDARICWA EWKMELCHTA KELKKYSNNN HFAYHTCNLS W RCGLKSTH IEVRLQASGG LVSMVAVMPN GTLIPIEGTR PTYWTEDSFA YLYDPAGTEK KTESTFLWCF KEHIRPTTEL SG AVYDTHY LGGTYDKNPQ FNYYCRDNGY YFELPANRLV CLPTSCYKRE GAIVNTMHPD TWKVSEKLHS ASQFDVNNVV HSL VYETEG LRLALSQLDH RFATLSRLFN RLTQSLAKID DRLLGTLLGQ DVSSKFISPT KFMLSPCLST PEGDSNCHNH SIYR DGRWV HNSDPTQCFS LSKSQPVDLY SFKELWLPQL LDVNVEGVVA DEEGWSFVAQ SKQALIDTMT YTKNGGKGTS LEDVL GYPS GWINGKLQGL LLNGAISWVV VIGVVLVGVC LMRRVF

UniProtKB: Envelope glycoprotein

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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