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- EMDB-26657: 50S E. coli ribosome bound to streptogramins VM2 and VS1 -

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Basic information

Entry
Database: EMDB / ID: EMD-26657
Title50S E. coli ribosome bound to streptogramins VM2 and VS1
Map data
Sample
  • Complex: 50S E. coli ribosome bound to streptogramins VM2 and VS1
KeywordsE. coli ribosome / streptogramin A / streptogramin B / antibiotics / RIBOSOME
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsPellegrino J / Lee DJ
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM123159 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124149 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128656 United States
CitationJournal: To Be Published
Title: 50S E. coli ribosome bound to streptogramins VM2 and VS1
Authors: Pellegrino J / Lee DJ / Seiple IB / Fraser JS
History
DepositionApr 14, 2022-
Header (metadata) releaseJun 8, 2022-
Map releaseJun 8, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26657.png

Downloads & links

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Map

FileDownload / File: emd_26657.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 500 pix.
= 332.5 Å		0.67 Å/pix.
x 500 pix.
= 332.5 Å		0.67 Å/pix.
x 500 pix.
= 332.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.665 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.481
Minimum - Maximum-8.927711 - 26.695955000000001
Average (Standard dev.)-0.008458151 (±0.85389036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 332.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_26657_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_26657_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 : 50S E. coli ribosome bound to streptogramins VM2 and VS1

EntireName: 50S E. coli ribosome bound to streptogramins VM2 and VS1
Components
  • Complex: 50S E. coli ribosome bound to streptogramins VM2 and VS1

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Supramolecule #1: 50S E. coli ribosome bound to streptogramins VM2 and VS1

SupramoleculeName: 50S E. coli ribosome bound to streptogramins VM2 and VS1
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 69.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134924
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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