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- EMDB-36912: Structure determination of SBA/GN2GN tubular assembly using cryo-EM -

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Basic information

Entry
Database: EMDB / ID: EMD-36912
TitleStructure determination of SBA/GN2GN tubular assembly using cryo-EM
Map data3D reconstruction of the tubular assembly of SBA/GN2GN
Sample
  • Complex: Helical complex of soybean agglutinin protein with GN2GN ligand
Keywordsprotein tube / self-assembly / polymorphism / protein-carbohydrate interaction / PLANT PROTEIN
Biological speciesGlycine max (soybean)
Methodhelical reconstruction / cryo EM / Resolution: 15.9 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: Structure determination of SBA/GN2GN tubular assembly using cryo-EM
Authors: Chen SY / Zhang L / Chen GS
History
DepositionJul 24, 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_36912.png

Downloads & links

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Map

FileDownload / File: emd_36912.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of the tubular assembly of SBA/GN2GN
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.61 Å/pix.
x 256 pix.
= 411.392 Å		1.61 Å/pix.
x 256 pix.
= 411.392 Å		1.61 Å/pix.
x 256 pix.
= 411.392 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.607 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.017327802 - 0.061435085
Average (Standard dev.)0.0017205719 (±0.008008845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 411.392 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 the SBA/GN2GN protein tube

Fileemd_36912_half_map_1.map
AnnotationEM half map of the 3D reconstruction of the SBA/GN2GN protein tube
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 the SBA/GN2GN protein tube

Fileemd_36912_half_map_2.map
AnnotationEM half map of the 3D reconstruction of the SBA/GN2GN protein tube
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helical complex of soybean agglutinin protein with GN2GN ligand

EntireName: Helical complex of soybean agglutinin protein with GN2GN ligand
Components
  • Complex: Helical complex of soybean agglutinin protein with GN2GN ligand

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Supramolecule #1: Helical complex of soybean agglutinin protein with GN2GN ligand

SupramoleculeName: Helical complex of soybean agglutinin protein with GN2GN 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
Processinghelical reconstruction
Aggregation statehelical 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: 50.0 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: 2.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 73000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 31.3 Å
Applied symmetry - Helical parameters - Δ&Phi: -134.3 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 15.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 49623
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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