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- EMDB-36928: Cryo-EM reconstruction of the pseudo-helical symmetric tubular as... -

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Basic information

Entry
Database: EMDB / ID: EMD-36928
TitleCryo-EM reconstruction of the pseudo-helical symmetric tubular assembly of SBA/GN5GN at 35 nm diameter
Map data3D reconstruction of the SBA/GN5GN tubular assembly
Sample
  • Complex: The tubular assembly of soybean agglutinin protein with GN5GN ligand
Keywordsprotein tube / self-assembly / polymorphism / protein-carbohydrate interaction / PLANT PROTEIN
Biological speciesGlycine max (soybean)
Methodsingle particle reconstruction / cryo EM / Resolution: 19.3 Å
AuthorsChen SY / Zhang L / Chen GS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)11774279 China
CitationJournal: To Be Published
Title: Cryo-EM reconstruction of the pseudo-helical symmetric tubular assembly of SBA/GN5GN at 35 nm diameter
Authors: Chen SY / Zhang L / Chen GS
History
DepositionJul 25, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36928.png

Downloads & links

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Map

FileDownload / File: emd_36928.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of the SBA/GN5GN tubular assembly
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 320 pix.
= 656.32 Å		2.05 Å/pix.
x 320 pix.
= 656.32 Å		2.05 Å/pix.
x 320 pix.
= 656.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.051 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.022710385 - 0.07614784
Average (Standard dev.)0.0010101683 (±0.008691378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 656.32007 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM half map of the 3D reconstruction of SBA/GN5GN tubular assembly

Fileemd_36928_half_map_1.map
AnnotationEM half map of the 3D reconstruction of SBA/GN5GN tubular assembly
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map of the 3D reconstruction of SBA/GN5GN tubular assembly

Fileemd_36928_half_map_2.map
AnnotationEM half map of the 3D reconstruction of SBA/GN5GN tubular assembly
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The tubular assembly of soybean agglutinin protein with GN5GN ligand

EntireName: The tubular assembly of soybean agglutinin protein with GN5GN ligand
Components
  • Complex: The tubular assembly of soybean agglutinin protein with GN5GN ligand

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Supramolecule #1: The tubular assembly of soybean agglutinin protein with GN5GN ligand

SupramoleculeName: The tubular assembly of soybean agglutinin protein with GN5GN ligand
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Glycine max (soybean)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 57000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 19.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 7292
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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