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- EMDB-61613: 50S subunit precursor state I -

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Basic information

Entry
Database: EMDB / ID: EMD-61613
Title50S subunit precursor state I
Map data50S subunit precursor State I
Sample
  • Complex: 50S subunit precursor State I
Keywords50S / precursor / assembly intermediate / RIBOSOME
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsSengupta S / Mukherjee R / Pilsl M / Bagale S / Adhikary AD / Borkar A / Pradeepkumar PI / Engel C / Chowdhury A / Kaushal PS / Anand R
Funding support United Kingdom, India, 3 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Science and Engineering Research Board (SERB) India
Department of Biotechnology (DBT, India) India
CitationJournal: Sci Adv / Year: 2025
Title: Mechanistic insights into 50 precursor recognition and targeting by erythromycin resistance methyltransferase.
Authors: Sombuddha Sengupta / Rajat Mukherjee / Michael Pilsl / Siddharam Bagale / Arijit Das Adhikary / Aditi N Borkar / Pushpangadan Indira Pradeepkumar / Christoph Engel / Arindam Chowdhury / Prem ...Authors: Sombuddha Sengupta / Rajat Mukherjee / Michael Pilsl / Siddharam Bagale / Arijit Das Adhikary / Aditi N Borkar / Pushpangadan Indira Pradeepkumar / Christoph Engel / Arindam Chowdhury / Prem S Kaushal / Ruchi Anand /
Abstract: Erythromycin resistance methyltransferases (Erms) confer resistance to macrolide, lincosamide, and streptogramin B antibiotics by methylating an internal base (A2058, numbering) in an elusive ...Erythromycin resistance methyltransferases (Erms) confer resistance to macrolide, lincosamide, and streptogramin B antibiotics by methylating an internal base (A2058, numbering) in an elusive precursor ribosomal state. Here, we capture the 50 ribosomal precursor-Erm complex by cryo-EM and show that a transient pocket formed in the early steps of ribosome biogenesis, situated 35 angstrom from the methylation site, serves as an anchor for the auxiliary C-terminal domain of Erm, thereby playing a crucial role in achieving specificity in this short-lived substrate with evolving structural features. Cryo-EM reveals that the catalytic Rossman fold of Erm undergoes a swaying motion to facilitate substrate scouting. Corroboratory smFRET studies show that for effective catalysis, Erm transitions between multiple conformations, an effective strategy adopted to orient the dynamic helix where methylation occurs. Unraveling this unique mechanism of targeting adopted by Erm paves the way for selective design of allosteric inhibitors directed toward reversing MLS resistance.
History
DepositionSep 21, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61613.png

Downloads & links

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Map

FileDownload / File: emd_61613.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation50S subunit precursor State I
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 480 pix.
= 331.2 Å		0.69 Å/pix.
x 480 pix.
= 331.2 Å		0.69 Å/pix.
x 480 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00497
Minimum - Maximum-0.0065004053 - 0.015690155
Average (Standard dev.)0.000050856324 (±0.000712142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61613_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_61613_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 subunit precursor State I

EntireName: 50S subunit precursor State I
Components
  • Complex: 50S subunit precursor State I

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Supramolecule #1: 50S subunit precursor State I

SupramoleculeName: 50S subunit precursor State I / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli K-12 (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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 41.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 11035
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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