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- EMDB-76892: 70S ribosome containing RpmE from Neisseria gonorrhoeae -

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Basic information

Entry
Database: EMDB / ID: EMD-76892
Title70S ribosome containing RpmE from Neisseria gonorrhoeae
Map data
Sample
  • Complex: 70S ribosome containing RpmE from Neisseria gonorrhoeae
Keywords70S / ribosome / RpmE
Biological speciesNeisseria gonorrhoeae FA 1090 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsMalezyna K / Forehand AL / Criss AK / Jomaa A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Alternative ribosomal protein RpmE2 is produced under zinc limitation in Neisseria gonorrhoeae and slows translation and bacterial growth
Authors: Forehand AL / Malezyna K / Thomas KS / Glomski IJ / Cornelissen CN / Jomaa A / Criss AK
History
DepositionApr 24, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76892.png

Downloads & links

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Map

FileDownload / File: emd_76892.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 450 pix.
= 414. Å		0.92 Å/pix.
x 450 pix.
= 414. Å		0.92 Å/pix.
x 450 pix.
= 414. Å

Surface

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Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0663
Minimum - Maximum-0.34484717 - 0.57968146
Average (Standard dev.)-0.00017175813 (±0.02912122)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 414.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76892_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #1

Fileemd_76892_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_76892_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : 70S ribosome containing RpmE from Neisseria gonorrhoeae

EntireName: 70S ribosome containing RpmE from Neisseria gonorrhoeae
Components
  • Complex: 70S ribosome containing RpmE from Neisseria gonorrhoeae

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Supramolecule #1: 70S ribosome containing RpmE from Neisseria gonorrhoeae

SupramoleculeName: 70S ribosome containing RpmE from Neisseria gonorrhoeae
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Neisseria gonorrhoeae FA 1090 (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

Concentration0.250 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.4 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 81249
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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