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- EMDB-60029: 4-start helix structure of SBA/Azo3GN3N3 microtube with a diamete... -

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Basic information

Entry
Database: EMDB / ID: EMD-60029
Title4-start helix structure of SBA/Azo3GN3N3 microtube with a diameter of about 32 nm
Map data
Sample
  • Complex: Helical complex of soybean agglutinin protein with Azo3GN3N3 ligand
    • Protein or peptide: soybean agglutinin
KeywordsSoybean Agglutinin / Azobenzene / Helical / Microtube / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesGlycine max (soybean)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsZhang Z / Chen G
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: 4-start helix structure of SBA/S3GN microtube with a diameter of about 32 nm
Authors: Zhang Z / Chen G
History
DepositionMay 6, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60029.png

Downloads & links

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Map

FileDownload / File: emd_60029.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 800 pix.
= 784. Å		0.98 Å/pix.
x 800 pix.
= 784. Å		0.98 Å/pix.
x 800 pix.
= 784. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.114
Minimum - Maximum-0.28252316 - 0.65834033
Average (Standard dev.)0.00035213065 (±0.03250142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 784.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60029_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_60029_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 : Helical complex of soybean agglutinin protein with Azo3GN3N3 ligand

EntireName: Helical complex of soybean agglutinin protein with Azo3GN3N3 ligand
Components
  • Complex: Helical complex of soybean agglutinin protein with Azo3GN3N3 ligand
    • Protein or peptide: soybean agglutinin

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Supramolecule #1: Helical complex of soybean agglutinin protein with Azo3GN3N3 ligand

SupramoleculeName: Helical complex of soybean agglutinin protein with Azo3GN3N3 ligand
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Glycine max (soybean)

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Macromolecule #1: soybean agglutinin

MacromoleculeName: soybean agglutinin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Glycine max (soybean)
SequenceString: AETVSFSWNK FVPKQPNMIL QGDAIVTSSG KLQLNKVDEN GTPKPSSLGR ALYSTPIHIW DKETGSVASF AASFNFTFYA PDTKRLADGL AFFLAPIDTK PQTHAGYLGL FNENESGDQV VAVEFDTFRN SWDPPNPHIG INVNSIRSIK TTSWDLANNK VAKVLITYDA ...String:
AETVSFSWNK FVPKQPNMIL QGDAIVTSSG KLQLNKVDEN GTPKPSSLGR ALYSTPIHIW DKETGSVASF AASFNFTFYA PDTKRLADGL AFFLAPIDTK PQTHAGYLGL FNENESGDQV VAVEFDTFRN SWDPPNPHIG INVNSIRSIK TTSWDLANNK VAKVLITYDA STSLLVASLV YPSQRTSNIL SDVVDLKTSL PEWVRIGFSA ATGLDIPGES HDVLSWSFAS NLPHASSNID PLDLTSFVLH EAI

UniProtKB: Lectin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

Concentration6 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134558
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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