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- EMDB-30380: Negative stain density of the tetrameric FRIL in solution -

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Basic information

Entry
Database: EMDB / ID: EMD-30380
TitleNegative stain density of the tetrameric FRIL in solution
Map dataNegative stain density of FRIL from lablab purpureus
Sample
  • Complex: FRIL in solution
    • Protein or peptide: FRIL
Biological speciesLablab purpureus (hyacinth bean)
Methodsingle particle reconstruction / Resolution: 27.59 Å
AuthorsChen T / Liu Y / Ma C
CitationJournal: Cell Rep / Year: 2020
Title: A Carbohydrate-Binding Protein from the Edible Lablab Beans Effectively Blocks the Infections of Influenza Viruses and SARS-CoV-2.
Authors: Yo-Min Liu / Md Shahed-Al-Mahmud / Xiaorui Chen / Ting-Hua Chen / Kuo-Shiang Liao / Jennifer M Lo / Yi-Min Wu / Meng-Chiao Ho / Chung-Yi Wu / Chi-Huey Wong / Jia-Tsrong Jan / Che Ma /
Abstract: The influenza virus hemagglutinin (HA) and coronavirus spike (S) protein mediate virus entry. HA and S proteins are heavily glycosylated, making them potential targets for carbohydrate binding agents ...The influenza virus hemagglutinin (HA) and coronavirus spike (S) protein mediate virus entry. HA and S proteins are heavily glycosylated, making them potential targets for carbohydrate binding agents such as lectins. Here, we show that the lectin FRIL, isolated from hyacinth beans (Lablab purpureus), has anti-influenza and anti-SARS-CoV-2 activity. FRIL can neutralize 11 representative human and avian influenza strains at low nanomolar concentrations, and intranasal administration of FRIL is protective against lethal H1N1 infection in mice. FRIL binds preferentially to complex-type N-glycans and neutralizes viruses that possess complex-type N-glycans on their envelopes. As a homotetramer, FRIL is capable of aggregating influenza particles through multivalent binding and trapping influenza virions in cytoplasmic late endosomes, preventing their nuclear entry. Remarkably, FRIL also effectively neutralizes SARS-CoV-2, preventing viral protein production and cytopathic effect in host cells. These findings suggest a potential application of FRIL for the prevention and/or treatment of influenza and COVID-19.
History
DepositionJul 14, 2020-
Header (metadata) releaseAug 26, 2020-
Map releaseAug 26, 2020-
UpdateAug 26, 2020-
Current statusAug 26, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 7.14
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30380.png

Downloads & links

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Map

FileDownload / File: emd_30380.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain density of FRIL from lablab purpureus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 80 pix.
= 164.8 Å		2.06 Å/pix.
x 80 pix.
= 164.8 Å		2.06 Å/pix.
x 80 pix.
= 164.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.14 / Movie #1: 7.14
Minimum - Maximum-1.4667897 - 15.700317
Average (Standard dev.)0.14859895 (±1.981077)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 164.79999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.062.062.06
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z164.800164.800164.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-1.46715.7000.149

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Supplemental data

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Sample components

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Entire : FRIL in solution

EntireName: FRIL in solution
Components
  • Complex: FRIL in solution
    • Protein or peptide: FRIL

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Supramolecule #1: FRIL in solution

SupramoleculeName: FRIL in solution / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Lablab purpureus (hyacinth bean)

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Macromolecule #1: FRIL

MacromoleculeName: FRIL / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Lablab purpureus (hyacinth bean)
SequenceString: MAQSLSFSFT KFDPNQEDLI FQGHATSTNN VLQLTKLDSA GNPVSSSAGR VLYSAPLRLW EDSAVLTSFD TIINFEISTP YTSRIADGLA FFIAPPDSVI SYHGGFLGLF PNANTLNNSS TSENQTTTKA ASSNVVAVEF DTYLNPDYGD PNYIHIGIDV NSIRSKVTAK ...String:
MAQSLSFSFT KFDPNQEDLI FQGHATSTNN VLQLTKLDSA GNPVSSSAGR VLYSAPLRLW EDSAVLTSFD TIINFEISTP YTSRIADGLA FFIAPPDSVI SYHGGFLGLF PNANTLNNSS TSENQTTTKA ASSNVVAVEF DTYLNPDYGD PNYIHIGIDV NSIRSKVTAK WDWQNGKIAT AHISYNSVSK RLSVTTYYPG SKPATLSYDI ELHTVLPEWV RVGLSASTGQ DKERNTVHSW SFTSSLWTNV AKKENENKYI TRGVLAS

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.4 / Details: PBS

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Number grids imaged: 2 / Number real images: 200 / Average exposure time: 0.8 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 340963
CTF correctionSoftware - Name: cisTEM
Final reconstructionNumber classes used: 50 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 27.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67041
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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