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- EMDB-38904: Local refinement of DSR2 tetramer bound with two DSAD1 inhibitors... -

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Basic information

Entry
Database: EMDB / ID: EMD-38904
TitleLocal refinement of DSR2 tetramer bound with two DSAD1 inhibitors on the opposite side
Map data
Sample
  • Complex: Complex of DSR2 tetramer and two DSAD1 inhibitors (opposite side)
KeywordsNADase / anti-phage defense / complex / immune evasion / IMMUNOSUPPRESSANT
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsWang RW / Xu Q / Wu ZX / Li JL / Shi ZB / Li FX
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370742 China
National Natural Science Foundation of China (NSFC)32271264 China
National Natural Science Foundation of China (NSFC)32200129 China
CitationJournal: To Be Published
Title: Local refinement of DSR2 tetramer bound with two DSAD1 inhibitors on the opposite side
Authors: Wang RW / Xu Q / Wu ZX / Li JL / Shi ZB / Li FX
History
DepositionJan 29, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38904.png

Downloads & links

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Map

FileDownload / File: emd_38904.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 430.92 Å		1.08 Å/pix.
x 400 pix.
= 430.92 Å		1.08 Å/pix.
x 400 pix.
= 430.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-1.8508874 - 3.6598105
Average (Standard dev.)0.00014082767 (±0.080727525)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 430.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38904_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38904_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 : Complex of DSR2 tetramer and two DSAD1 inhibitors (opposite side)

EntireName: Complex of DSR2 tetramer and two DSAD1 inhibitors (opposite side)
Components
  • Complex: Complex of DSR2 tetramer and two DSAD1 inhibitors (opposite side)

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Supramolecule #1: Complex of DSR2 tetramer and two DSAD1 inhibitors (opposite side)

SupramoleculeName: Complex of DSR2 tetramer and two DSAD1 inhibitors (opposite side)
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

Concentration0.5 mg/mL
BufferpH: 7.5 / Details: 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 13000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91205
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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