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- EMDB-0736: 1-start helix structure of SBA/GN3GN microtube with a diameter of... -

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Basic information

Entry
Database: EMDB / ID: EMD-0736
Title1-start helix structure of SBA/GN3GN microtube with a diameter of about 29 nm
Map dataSBA/GN3GN microtube
Sample
  • Complex: Helical complex of soybean agglutinin protein with GN3GN ligand
Biological speciesGlycine max (soybean)
Methodhelical reconstruction / cryo EM / Resolution: 10.9 Å
AuthorsZhang L / Chen GS / Chen SY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China11774279 China
CitationJournal: J Am Chem Soc / Year: 2019
Title: Chemically Controlled Helical Polymorphism in Protein Tubes by Selective Modulation of Supramolecular Interactions.
Authors: Zhen Li / Shuyu Chen / Chendi Gao / Zhiwei Yang / Kuo-Chih Shih / Zdravko Kochovski / Guang Yang / Lu Gou / Mu-Ping Nieh / Ming Jiang / Lei Zhang / Guosong Chen /
Abstract: Polymorphism has been the subject of investigation across different research disciplines. In biology, polymorphism could be interpreted in such a way that discrete biomacromolecules can adopt ...Polymorphism has been the subject of investigation across different research disciplines. In biology, polymorphism could be interpreted in such a way that discrete biomacromolecules can adopt diversiform specific conformations/packing arrangement, and this polymorph-dependent property is essential for many biochemical processes. For example, bacterial flagellar filament, composed of flagellin, switches between different supercoiled state allowing the bacteria to swim and tumble. However, in artificial supramolecular systems, it is often challenging to achieve polymorph control and prediction, and in most cases, two or more concomitant polymorphs of similar formation energies coexist. Here, we show that a tetrameric protein with properly oriented binding sites on its surface can arrange into diverse protein tubes with distinct helical parameters by adding specifically designed inducing ligands. We examined several parameters of the ligand that would influence the protein tube formation and found that the flexibility of the ligand linker and the dimerization pose of the ligand complex is critical for the successful production of the tubes and eventually influence the specific helical polymorphs of the formed tubes. A surface lattice accommodation model was further developed to rationalize the geometrical relationship between each helical tube type. Molecular simulation was used to elucidate the interactions between ligands and SBA and molecular basis for polymorphic switching of the protein tubes. Moreover, the kinetics of structural formation was studied and the ligand design was found that can affect the kinetics of the protein polymerization pathway. In short, our designed protein tubes serves as an enlightening system for understanding how a protein polymer composed of a single protein switches among different helical states.
History
DepositionAug 10, 2019-
Header (metadata) releaseJun 24, 2020-
Map releaseJun 24, 2020-
UpdateJun 24, 2020-
Current statusJun 24, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0376
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0376
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0736.png

Downloads & links

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Map

FileDownload / File: emd_0736.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSBA/GN3GN microtube
Voxel sizeX=Y=Z: 2.051 Å
Density
Contour LevelBy AUTHOR: 0.0376 / Movie #1: 0.0376
Minimum - Maximum-0.028680006 - 0.082837194
Average (Standard dev.)0.0031631019 (±0.012558065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 525.056 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.0512.0512.051
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z525.056525.056525.056
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-0.0290.0830.003

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Supplemental data

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Sample components

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Entire : Helical complex of soybean agglutinin protein with GN3GN ligand

EntireName: Helical complex of soybean agglutinin protein with GN3GN ligand
Components
  • Complex: Helical complex of soybean agglutinin protein with GN3GN ligand

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Supramolecule #1: Helical complex of soybean agglutinin protein with GN3GN ligand

SupramoleculeName: Helical complex of soybean agglutinin protein with GN3GN ligand
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 7.217 Å
Applied symmetry - Helical parameters - Δ&Phi: -38.899 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 10.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7789
FSC plot (resolution estimation)

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