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

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Open data


ID or keywords:

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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: To Be Published
Title: Mechanistic Insights into 50S Precursor Recognition and Targeting by Erythromycin Resistance Methyltransferase
Authors: Sengupta S / Mukherjee R / Pilsl M / Bagale S / Adhikary AD / Borkar A / Pradeepkumar PI / Engel C / Chowdhury A / Kaushal PS / Anand R
History
DepositionSep 21, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 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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