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- EMDB-47909: Cryo-EM structure of the ribosome-tunnel occluding hibernation fa... -

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Basic information

Entry
Database: EMDB / ID: EMD-47909
TitleCryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to Mycobacterium tuberculosis C- 70S ribosome
Map dataCryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to Mycobacterium tuberculosis C- 70S ribosome
Sample
  • Complex: Ribosome-tunnel occluding hibernation factor bound to Mycobacterium tuberculosis C- 70S ribosome
Keywordshibernating ribosome / Mycobacterium tuberculosis / nascent peptide exit tunnel / 70S / hibernation factor / TRANSLATION / RIBOSOME
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsMajumdar S / Ojha AK / Agrawal RK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32422 United States
CitationJournal: Biorxiv / Year: 2024
Title: A Novel Actinobacteria-Specific Ribosome Hibernation Factor in Mycobacterium tuberculosis
Authors: Majumdar S / Li Y / Manjari SR / Gamper HB / Hou YM / Banavali NK / Ojha AK / Agrawal RK
History
DepositionNov 14, 2024-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47909.png

Downloads & links

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Map

FileDownload / File: emd_47909.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to Mycobacterium tuberculosis C- 70S ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 429.2 Å		1.07 Å/pix.
x 400 pix.
= 429.2 Å		1.07 Å/pix.
x 400 pix.
= 429.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.073 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.221 - 2.80062
Average (Standard dev.)-0.0011946914 (±0.10241632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 429.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of the ribosome-tunnel occluding hibernation factor...

Fileemd_47909_half_map_1.map
AnnotationCryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to Mycobacterium tuberculosis C- 70S ribosome-half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the ribosome-tunnel occluding hibernation factor...

Fileemd_47909_half_map_2.map
AnnotationCryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to Mycobacterium tuberculosis C- 70S ribosome-half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ribosome-tunnel occluding hibernation factor bound to Mycobacteri...

EntireName: Ribosome-tunnel occluding hibernation factor bound to Mycobacterium tuberculosis C- 70S ribosome
Components
  • Complex: Ribosome-tunnel occluding hibernation factor bound to Mycobacterium tuberculosis C- 70S ribosome

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Supramolecule #1: Ribosome-tunnel occluding hibernation factor bound to Mycobacteri...

SupramoleculeName: Ribosome-tunnel occluding hibernation factor bound to Mycobacterium tuberculosis C- 70S ribosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#55
Source (natural)Organism: Mycobacterium tuberculosis (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

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
95.0 mMKClPotassium chloride
5.0 mMNH4ClAmmonum chloride
5.0 mMMg(OAC)2Magnesium acetate
0.5 mMCaCl2Calcium chloride
8.0 mMPutrescine
1.0 mMSpermidine
5.0 mMKPPotassium phosphate
1.0 mMDithiotreitol

Details: Polymix buffer
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: Leginon
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 13499 / Average electron dose: 50.75 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5471811
CTF correctionSoftware - Name: cryoSPARC (ver. v4.4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.4.0) / Number images used: 36537
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v4.4.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v4.4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7mt7


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 41.3 / Target criteria: Cross-corelation coefficient

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