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- EMDB-8065: Soybean agglutinin(SBA) microtube -

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Basic information

Entry
Database: EMDB / ID: EMD-8065
TitleSoybean agglutinin(SBA) microtube
Map dataNone
Sample
  • Complex: soybean agglutinin microtube
Biological speciesGlycine max (soybean)
Methodhelical reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsZhang X / Li X / Liu C
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China91227203, 51322306, 31470748 and GZ962 China
Tsinghua-Peking Jonit center for life sciences China
State High-Tech Development Plan2015AA020907, 2015AA020914 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
DepositionFeb 2, 2016-
Header (metadata) releaseDec 14, 2016-
Map releaseFeb 8, 2017-
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: 0.0706
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0706
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8065.png

Downloads & links

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Map

FileDownload / File: emd_8065.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 2.64 Å
Density
Contour LevelBy AUTHOR: 0.0706 / Movie #1: 0.0706
Minimum - Maximum-0.05710962 - 0.14543343
Average (Standard dev.)-0.0245803 (±0.026232077)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 633.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.642.642.64
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z633.600633.600633.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0570.145-0.025

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Supplemental data

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Sample components

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Entire : soybean agglutinin microtube

EntireName: soybean agglutinin microtube
Components
  • Complex: soybean agglutinin microtube

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Supramolecule #1: soybean agglutinin microtube

SupramoleculeName: soybean agglutinin microtube / type: complex / ID: 1 / Parent: 0
Details: soybean agglutinin tetramer linked by the designed ligands
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
GridModel: Qutantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2 / Details: Images were collected with 4 frames per second
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: OTHER / Details: cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: FREALIGN
Details: Local refinement was performed using FREALIGN mode 1
Final reconstructionApplied symmetry - Helical parameters - Δz: 21.22 Å
Applied symmetry - Helical parameters - Δ&Phi: -36.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 8.09) / Number images used: 63925

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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