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- EMDB-34879: The nanotube of Ralstonia solanacearum lectin(RSL) induced by F3R -

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Basic information

Entry
Database: EMDB / ID: EMD-34879
TitleThe nanotube of Ralstonia solanacearum lectin(RSL) induced by F3R
Map datathe nanotube of Ralstonia solanacearum lectin(RSL) induced by F3R
Sample
  • Complex: The nanotube of Ralstonia solanacearum lectin(RSL) induced by F3R
    • Other: Ralstonia solanacearum lectin (RSL)
KeywordsFucose binding protein / Ralstonia solanacearum lectin / SUGAR BINDING PROTEIN
Biological speciesRalstonia solanacearum (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 16.4 Å
AuthorsLi L / Chen G
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: ACS Nano / Year: 2023
Title: Spatiotemporal Landscape for the Sophisticated Transformation of Protein Assemblies Defined by Multiple Supramolecular Interactions.
Authors: Long Li / Zhen Li / Ziying Wang / Shuyu Chen / Rongying Liu / Xuyang Xu / Zhi Zhang / Linfei Ye / Yu Ding / Quan Luo / Sheng Cao / Lei Zhang / Anne Imberty / Guosong Chen /
Abstract: Precise protein assemblies not only constitute a series of living machineries but also provide an advanced class of biomaterials. Previously, we developed the inducing ligand strategy to generate ...Precise protein assemblies not only constitute a series of living machineries but also provide an advanced class of biomaterials. Previously, we developed the inducing ligand strategy to generate various fixed protein assemblies, without the formation of noncovalent interactions between proteins. Here, we demonstrated that controlling the symmetry and number of supramolecular interactions introduced on protein surfaces could direct the formation of unspecific interactions between proteins and induce various nanoscale assemblies, including coiling nanowires, nanotubes, and nanosheets, without manipulation of the protein's native surfaces. More importantly, these nanoscale assemblies could spontaneously evolve into more ordered architectures, crystals. We further showed that the transformation from the introduced supramolecular interactions to the interactions formed between proteins was crucial for pathway selection and outcomes of evolution. These findings reveal a transformation mechanism of protein self-assembly that has not been exploited before and may provide an approach to generate complex and transformable biomacromolecular self-assemblies.
History
DepositionNov 30, 2022-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34879.png

Downloads & links

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Map

FileDownload / File: emd_34879.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe nanotube of Ralstonia solanacearum lectin(RSL) induced by F3R
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.98 Å/pix.
x 224 pix.
= 891. Å		3.98 Å/pix.
x 224 pix.
= 891. Å		3.98 Å/pix.
x 224 pix.
= 891. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.97768 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.19044976 - 0.3702341
Average (Standard dev.)0.0019315644 (±0.03106478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 891.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 2

Fileemd_34879_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_34879_half_map_2.map
AnnotationHalf map 1
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 nanotube of Ralstonia solanacearum lectin(RSL) induced by F3R

EntireName: The nanotube of Ralstonia solanacearum lectin(RSL) induced by F3R
Components
  • Complex: The nanotube of Ralstonia solanacearum lectin(RSL) induced by F3R
    • Other: Ralstonia solanacearum lectin (RSL)

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Supramolecule #1: The nanotube of Ralstonia solanacearum lectin(RSL) induced by F3R

SupramoleculeName: The nanotube of Ralstonia solanacearum lectin(RSL) induced by F3R
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ralstonia solanacearum (bacteria)

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Macromolecule #1: Ralstonia solanacearum lectin (RSL)

MacromoleculeName: Ralstonia solanacearum lectin (RSL) / type: other / ID: 1 / Classification: cyclic-pseudo-peptide
Source (natural)Organism: Ralstonia solanacearum (bacteria)
SequenceString: MSSVQTAATS WGTVPSIAVY TANNGKITER CWDGKGWYTG AFNEPGDNVS VTSWLVGSAI HIRVYASTGT TTTEWCWDGN GWTKGAYTSS TVPGDQTAAT SWGTVPSIAV YTANNGKITE RCWDGKGWYT GAFNEPGDNV SVTSWLVGSA IHIRVYASTG TTTTEWCWDG ...String:
MSSVQTAATS WGTVPSIAVY TANNGKITER CWDGKGWYTG AFNEPGDNVS VTSWLVGSAI HIRVYASTGT TTTEWCWDGN GWTKGAYTSS TVPGDQTAAT SWGTVPSIAV YTANNGKITE RCWDGKGWYT GAFNEPGDNV SVTSWLVGSA IHIRVYASTG TTTTEWCWDG NGWTKGAYTS STVPGDQTAA TSWGTVPSIA VYTANNGKIT ERCWDGKGWY TGAFNEPGDN VSVTSWLVGS AIHIRVYAST GTTTTEWCWD GNGWTKGAYT AT
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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: 7.5 / Details: 20mM Tris-HCl,100mM NaCl
GridModel: Quantifoil R2/1 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 6.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 25.5 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 16.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9729
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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