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- EMDB-60012: The cryoEM reconstruction of H5N1 HA asymmetric filament in confo... -

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Basic information

Entry
Database: EMDB / ID: EMD-60012
TitleThe cryoEM reconstruction of H5N1 HA asymmetric filament in conformation B
Map data
Sample
  • Complex: Single trimer of H5N1 HA-FabH5M9 complex
    • Complex: FabH5M9
    • Complex: H5N1 hemagglutinin
KeywordsInfluenza / glycosylation / sialic acid / VIRAL PROTEIN
Biological speciesInfluenza A virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.19 Å
AuthorsLi R / Gao J / Wang L / Gui M / Xiang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Multivalent interactions between fully glycosylated influenza virus hemagglutinins mediated by glycans at distinct N-glycosylation sites
Authors: Li R / Gao J / Wang L / Gui M / Xiang Y
History
DepositionMay 3, 2024-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60012.png

Downloads & links

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Map

FileDownload / File: emd_60012.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 400 pix.
= 528. Å		1.32 Å/pix.
x 400 pix.
= 528. Å		1.32 Å/pix.
x 400 pix.
= 528. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.438
Minimum - Maximum-2.3228877 - 3.9412575
Average (Standard dev.)-0.00032179418 (±0.07342993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60012_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_60012_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 : Single trimer of H5N1 HA-FabH5M9 complex

EntireName: Single trimer of H5N1 HA-FabH5M9 complex
Components
  • Complex: Single trimer of H5N1 HA-FabH5M9 complex
    • Complex: FabH5M9
    • Complex: H5N1 hemagglutinin

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Supramolecule #1: Single trimer of H5N1 HA-FabH5M9 complex

SupramoleculeName: Single trimer of H5N1 HA-FabH5M9 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 200 KDa

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Supramolecule #2: FabH5M9

SupramoleculeName: FabH5M9 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: H5N1 hemagglutinin

SupramoleculeName: H5N1 hemagglutinin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4mhh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60487
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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