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- EMDB-55016: Multibody refinement of pooled Ribosome-Sec translocon-Dome super... -

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Basic information

Entry
Database: EMDB / ID: EMD-55016
TitleMultibody refinement of pooled Ribosome-Sec translocon-Dome supercomplexes from four antibiotic treated Mycoplasma pneumoniae datasets, body 1/3
Map data
Sample
  • Cell: pooled Ribosome-Sec translocon-Dome supercomplexes from four antibiotic treated Mycoplasma pneumoniae datasets(chloramphenicol treated & on K2 camera; puseudoridimycin treated; spectinomycin treated; chloramphenicol treated & on K3 camera)
KeywordsRibosome / Translocation / Chaperone / Antibiotics / TRANSLATION
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 11.0 Å
AuthorsXue L / Jensen R / Mahamid J
Funding support United States, Germany, China, Denmark, 4 items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative2021-234620 United States
German Research Foundation (DFG)426290502 Germany
Ministry of Science and Technology (MoST, China)2024YFA1306200 China
Independent Research Fund Denmark - Medical Sciences0164-00010A Denmark
CitationJournal: To Be Published
Title: In-cell discovery and characterization of a non-canonical bacterial protein translocation-folding complex
Authors: Jensen R / Xue L / Marotta F / Somody JC / Selkrig J / Lenz S / Rappsilber J / Savitski MM / Kosinski J / Typas A / Zimmermann-Kogadeeva M / Bork P / Mahamid J
History
DepositionSep 5, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55016.png

Downloads & links

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Map

FileDownload / File: emd_55016.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.9 Å/pix.
x 256 pix.
= 742.4 Å		2.9 Å/pix.
x 256 pix.
= 742.4 Å		2.9 Å/pix.
x 256 pix.
= 742.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.67
Minimum - Maximum-0.8408913 - 1.607892
Average (Standard dev.)0.0032713455 (±0.050035812)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 742.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55016_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: #2

Fileemd_55016_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55016_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 : pooled Ribosome-Sec translocon-Dome supercomplexes from four anti...

EntireName: pooled Ribosome-Sec translocon-Dome supercomplexes from four antibiotic treated Mycoplasma pneumoniae datasets(chloramphenicol treated & on K2 camera; puseudoridimycin treated; spectinomycin ...Name: pooled Ribosome-Sec translocon-Dome supercomplexes from four antibiotic treated Mycoplasma pneumoniae datasets(chloramphenicol treated & on K2 camera; puseudoridimycin treated; spectinomycin treated; chloramphenicol treated & on K3 camera)
Components
  • Cell: pooled Ribosome-Sec translocon-Dome supercomplexes from four antibiotic treated Mycoplasma pneumoniae datasets(chloramphenicol treated & on K2 camera; puseudoridimycin treated; spectinomycin treated; chloramphenicol treated & on K3 camera)

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Supramolecule #1: pooled Ribosome-Sec translocon-Dome supercomplexes from four anti...

SupramoleculeName: pooled Ribosome-Sec translocon-Dome supercomplexes from four antibiotic treated Mycoplasma pneumoniae datasets(chloramphenicol treated & on K2 camera; puseudoridimycin treated; spectinomycin ...Name: pooled Ribosome-Sec translocon-Dome supercomplexes from four antibiotic treated Mycoplasma pneumoniae datasets(chloramphenicol treated & on K2 camera; puseudoridimycin treated; spectinomycin treated; chloramphenicol treated & on K3 camera)
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
Details: Modified Hayflick medium: 14.7g/l Difco PPLO(Becton Dickinson), 20% (v/v) Gibco horse serum (New Zealand origin), 100 mM HEPES-Na; pH 7.4, 1% (w/w) glucose, 0.002% (w/w) phenol red, 1000 U/ml penicillin G.
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Back-side blotting for 2-3 seconds before plunging using a manual plunger without an environmental control chamber..
DetailsMycoplasma pneumoniae M129 cells were grown on gold Quantifoil grids at 37 Celsius in modified Hayflick medium. Treatment with different antibiotics for 15-20 minutes before plunge freezing.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Average electron dose: 3.2 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Average electron dose: 3.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 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

Image recording ID2
DetailsData collected on both GATAN K2 and K3 camera were combined for averaging
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number subtomograms used: 2304
ExtractionNumber tomograms: 360 / Number images used: 77980 / Software: (Name: PyTom, Warp (ver. 1.0.9))
Details: Ribosome-Sec translocon-Dome supercomplex in chloramphenicol treated Mycoplasma pneumoniae cells by K2 camera: 18957 sub-tomograms from 65 tomograms Ribosome-Sec translocon-Dome supercomplex ...Details: Ribosome-Sec translocon-Dome supercomplex in chloramphenicol treated Mycoplasma pneumoniae cells by K2 camera: 18957 sub-tomograms from 65 tomograms Ribosome-Sec translocon-Dome supercomplex in puseudoridimycin treated Mycoplasma pneumoniae cells : 15314 sub-tomograms from 86 tomograms ribosome-cage supercomplexs in spectinomycin-treated Mycoplasma pneumoniae cells: 12935 sub-tomograms from 70 tomograms; ribosome-cage supercomplexs in chlooramphenicol-treated Mycoplasma pneumoniae cells by K3 camera: 30774 sub-tomograms from 139 tomograms
CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: PHASE FLIPPING ONLY
Final 3D classificationSoftware - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
FSC plot (resolution estimation)

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