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- EMDB-35112: Cryo-EM map of SepF -

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Basic information

Entry
Database: EMDB / ID: EMD-35112
TitleCryo-EM map of SepF
Map data
Sample
  • Complex: SepF from Bacillus subtilis
KeywordsCell division FtsZ dependent cytokinesis Septation / CYTOSOLIC PROTEIN
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.32 Å
AuthorsZhang HW / Zhang C / Chang ZW / Yang J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900046 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Molecular basis for curvature formation in SepF polymerization.
Authors: Wenjing Liu / Chang Zhang / Huawei Zhang / Shaojie Ma / Jing Deng / Daping Wang / Ziwei Chang / Jun Yang /
Abstract: The self-assembly of proteins into curved structures plays an important role in many cellular processes. One good example of this phenomenon is observed in the septum-forming protein (SepF), which ...The self-assembly of proteins into curved structures plays an important role in many cellular processes. One good example of this phenomenon is observed in the septum-forming protein (SepF), which forms polymerized structures with uniform curvatures. SepF is essential for regulating the thickness of the septum during bacteria cell division. In , SepF polymerization involves two distinct interfaces, the β-β and α-α interfaces, which define the assembly unit and contact interfaces, respectively. However, the mechanism of curvature formation in this step is not yet fully understood. In this study, we employed solid-state NMR (SSNMR) to compare the structures of cyclic wild-type SepF assemblies with linear assemblies resulting from a mutation of G137 on the β-β interface. Our results demonstrate that while the sequence differences arise from the internal assembly unit, the dramatic changes in the shape of the assemblies depend on the α-α interface between the units. We further provide atomic-level insights into how the angular variation of the α2 helix on the α-α interface affects the curvature of the assemblies, using a combination of SSNMR, cryo-electron microscopy, and simulation methods. Our findings shed light on the shape control of protein assemblies and emphasize the importance of interhelical contacts in retaining curvature.
History
DepositionJan 11, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35112.png

Downloads & links

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Map

FileDownload / File: emd_35112.map.gz / Format: CCP4 / Size: 37.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.829 Å
Density
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.27040192 - 0.6715133
Average (Standard dev.)0.0042205616 (±0.038818132)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions214214214
Spacing214214214
CellA=B=C: 177.406 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35112_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_35112_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 : SepF from Bacillus subtilis

EntireName: SepF from Bacillus subtilis
Components
  • Complex: SepF from Bacillus subtilis

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Supramolecule #1: SepF from Bacillus subtilis

SupramoleculeName: SepF from Bacillus subtilis / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bacillus subtilis (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 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: 1.5 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3zih

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19649
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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