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- EMDB-56520: Cryo-EM map of SKM-70S complex State 2 (Accommodating A-tRNA) -

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Basic information

Entry
Database: EMDB / ID: EMD-56520
TitleCryo-EM map of SKM-70S complex State 2 (Accommodating A-tRNA)
Map dataMain map, postprocessed, of SKM-bound complex State II
Sample
  • Complex: Cryo-EM structure of SKM-70S ribosomal stalled complex in the major state (vacant A-site, canon)
KeywordsAntibiotics / 70S complex / Body closure / Accomodation / RIBOSOME
Biological speciesEscherichia coli B (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsMorici M / Corazza M / Safdari HA / Wilson DN
Funding support United States, Canada, Germany, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 GM127134 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)NIH R01 AI162961 United States
Canadian Institutes of Health Research (CIHR)FDN148463 Canada
German Research Foundation (DFG)WI3285/12-1 Germany
CitationJournal: To Be Published
Title: Saskemycin, a potent antimycobacterial agent targeting a unique site in the ribosome
Authors: Cook MA / Xu M / Wang W / Rao VN / Schaenzer AJ / Wang L / Yarlagadda V / Guitor AK / Ejim L / Wright G / Golas AJ / Nietupski RM / Fitzgerald M / Hung DT / Sahile H / Av-Gay Y / Lin S / ...Authors: Cook MA / Xu M / Wang W / Rao VN / Schaenzer AJ / Wang L / Yarlagadda V / Guitor AK / Ejim L / Wright G / Golas AJ / Nietupski RM / Fitzgerald M / Hung DT / Sahile H / Av-Gay Y / Lin S / Dhar N / Travin D / Klepacki D / Vazquez-Laslop N / Mankin A / Morici M / Corazza M / Safdari HA / Berger M / Wilson DN
History
DepositionJan 30, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56520.png

Downloads & links

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Map

FileDownload / File: emd_56520.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map, postprocessed, of SKM-bound complex State II
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 432 pix.
= 359.424 Å		0.83 Å/pix.
x 432 pix.
= 359.424 Å		0.83 Å/pix.
x 432 pix.
= 359.424 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0162
Minimum - Maximum-0.05829187 - 0.14469962
Average (Standard dev.)0.00044067652 (±0.0038038103)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 359.424 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1 used to generate the postprocessed main map

Fileemd_56520_half_map_1.map
AnnotationHalf map 1 used to generate the postprocessed main map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 used to generate the postprocessed main map

Fileemd_56520_half_map_2.map
AnnotationHalf map 2 used to generate the postprocessed main 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 : Cryo-EM structure of SKM-70S ribosomal stalled complex in the maj...

EntireName: Cryo-EM structure of SKM-70S ribosomal stalled complex in the major state (vacant A-site, canon)
Components
  • Complex: Cryo-EM structure of SKM-70S ribosomal stalled complex in the major state (vacant A-site, canon)

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Supramolecule #1: Cryo-EM structure of SKM-70S ribosomal stalled complex in the maj...

SupramoleculeName: Cryo-EM structure of SKM-70S ribosomal stalled complex in the major state (vacant A-site, canon)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#55
Source (natural)Organism: Escherichia coli B (bacteria)
Molecular weightTheoretical: 2.5 MDa

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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: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.14 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Molmap generated by a modified version of the pdb 7K00, containing no sample-specific component (deleted drugs, no tRNAs, no mRNA).
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 312833
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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