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- EMDB-76891: 70S ribosome containing RpmE2 from Neisseria gonorrhoeae -

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Basic information

Entry
Database: EMDB / ID: EMD-76891
Title70S ribosome containing RpmE2 from Neisseria gonorrhoeae
Map data
Sample
  • Complex: 70S ribosome containing RpmE2 from Neisseria gonorrhoeae
Keywords70S / ribosome / RpmE2
Biological speciesNeisseria gonorrhoeae FA 1090 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 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: mBio / Year: 2026
Title: Alternative ribosomal protein RpmE2 is produced under zinc limitation in and slows translation and bacterial growth.
Authors: Amy L Forehand / Kinga Malezyna / Keena S Thomas / Ian J Glomski / Cynthia Nau Cornelissen / Ahmad Jomaa / Alison K Criss /
Abstract: To enhance its pathogenic potential, (Gc) pirates zinc from human metal sequestration proteins using TonB-dependent outer membrane transport systems. However, cytoplasmic mechanisms by which Gc ...To enhance its pathogenic potential, (Gc) pirates zinc from human metal sequestration proteins using TonB-dependent outer membrane transport systems. However, cytoplasmic mechanisms by which Gc adapts to zinc limitation are still uncharacterized. and transcripts, encoding alternative L31 and L36 ribosomal proteins, respectively, which are not predicted to bind zinc, are significantly more abundant in zinc-limited Gc. In other bacterial species, alternative ribosomal proteins replace canonical zinc-binding ribosomal proteins when zinc availability is low, enabling growth under metal limitation. We found that Gc and are in an operon and transcriptionally induced under zinc limitation by derepression via the zinc uptake regulator Zur, while genes encoding canonical proteins and are not zinc-regulated. In contrast to other bacteria, ribosomes in zinc-limited Gc contained both RpmE2 and RpmE. Furthermore, Gc deleted for RpmE2 and RpmJ2 grew better than the wild-type parent under zinc limitation. Gc engineered to produce only RpmE2 exhibited a growth defect relative to RpmE-only Gc, regardless of zinc availability. Moreover, ribosomes from RpmE2-only Gc had reduced translation . Thus, unlike other bacteria, the alternative L31 protein RpmE2 is not functionally equivalent to the canonical RpmE in Gc. Instead, the ribosomes of zinc-limited Gc are heterogeneous, containing either alternative or canonical ribosomal proteins. We propose that L31 ribosomal protein alternation allows Gc to withstand zinc limitation by reducing translation and slowing growth, to prolong its survival when encountering host-imposed nutritional immunity.
IMPORTANCE: Zinc acquisition is crucial for growth and infectivity of (Gc). However, research on Gc adaptation to zinc limitation has primarily focused on outer and inner membrane zinc transporters. ...IMPORTANCE: Zinc acquisition is crucial for growth and infectivity of (Gc). However, research on Gc adaptation to zinc limitation has primarily focused on outer and inner membrane zinc transporters. Here, we implicate ribosomal protein alternation in the Gc response to zinc limitation. Ribosomes containing the non-zinc-binding, alternative ribosomal protein RpmE2 are less translationally active, and RpmE2-producing bacteria grow more slowly. This contrasts with reports from other bacteria, where ribosomal protein alternation facilitates growth in zinc-limited conditions. This work uncovers a new way in which ribosomal protein alternation enables bacterial resistance to nutritional immunity.
History
DepositionApr 24, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76891.png

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Map

FileDownload / File: emd_76891.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 512 pix.
= 471.04 Å		0.92 Å/pix.
x 512 pix.
= 471.04 Å		0.92 Å/pix.
x 512 pix.
= 471.04 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
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Contour LevelBy AUTHOR: 0.0704
Minimum - Maximum-0.3436156 - 0.59907776
Average (Standard dev.)-0.00096484844 (±0.028881673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 471.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76891_msk_1.map
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Half map: #1

Fileemd_76891_half_map_1.map
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Half map: #2

Fileemd_76891_half_map_2.map
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Sample components

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Entire : 70S ribosome containing RpmE2 from Neisseria gonorrhoeae

EntireName: 70S ribosome containing RpmE2 from Neisseria gonorrhoeae
Components
  • Complex: 70S ribosome containing RpmE2 from Neisseria gonorrhoeae

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Supramolecule #1: 70S ribosome containing RpmE2 from Neisseria gonorrhoeae

SupramoleculeName: 70S ribosome containing RpmE2 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: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 95434
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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