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- EMDB-3664: Structure of the Bacillus subtilis hibernating 100S ribosome reve... -

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Entry
Database: EMDB / ID: EMD-3664
TitleStructure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.
Map dataCryo-EM structure of the Bacillus subtilis 100S ribosome, filtered and masked final map
Sample
  • Complex: Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsBeckert B / Abdelshahid M / Schafer H / Steinchen W / Arenz S / Berninghausen O / Beckmann R / Bange G / Turgay K / Wilson DN
CitationJournal: EMBO J / Year: 2017
Title: Structure of the hibernating 100S ribosome reveals the basis for 70S dimerization.
Authors: Bertrand Beckert / Maha Abdelshahid / Heinrich Schäfer / Wieland Steinchen / Stefan Arenz / Otto Berninghausen / Roland Beckmann / Gert Bange / Kürşad Turgay / Daniel N Wilson /
Abstract: Under stress conditions, such as nutrient deprivation, bacteria enter into a hibernation stage, which is characterized by the appearance of 100S ribosomal particles. In , dimerization of 70S ...Under stress conditions, such as nutrient deprivation, bacteria enter into a hibernation stage, which is characterized by the appearance of 100S ribosomal particles. In , dimerization of 70S ribosomes into 100S requires the action of the ribosome modulation factor (RMF) and the hibernation-promoting factor (HPF). Most other bacteria lack RMF and instead contain a long form HPF (LHPF), which is necessary and sufficient for 100S formation. While some structural information exists as to how RMF and HPF mediate formation of 100S (100S), structural insight into 100S formation by LHPF has so far been lacking. Here we present a cryo-EM structure of the hibernating 100S (100S), revealing that the C-terminal domain (CTD) of the LHPF occupies a site on the 30S platform distinct from RMF Moreover, unlike RMF, the HPF-CTD is directly involved in forming the dimer interface, thereby illustrating the divergent mechanisms by which 100S formation is mediated in the majority of bacteria that contain LHPF, compared to some γ-proteobacteria, such as .
History
DepositionApr 11, 2017-
Header (metadata) releaseMay 31, 2017-
Map releaseMay 31, 2017-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3664.png

Downloads & links

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Map

FileDownload / File: emd_3664.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the Bacillus subtilis 100S ribosome, filtered and masked final map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 540 pix.
= 585.36 Å		1.08 Å/pix.
x 540 pix.
= 585.36 Å		1.08 Å/pix.
x 540 pix.
= 585.36 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.031828254 - 0.08945265
Average (Standard dev.)0.0008286616 (±0.005482241)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 585.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z540540540
origin x/y/z0.0000.0000.000
length x/y/z585.360585.360585.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS540540540
D min/max/mean-0.0320.0890.001

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Supplemental data

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Additional map: Cryo-EM structure of the Bacillus subtilis 100S ribosome,...

Fileemd_3664_additional.map
AnnotationCryo-EM structure of the Bacillus subtilis 100S ribosome, filtered final map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryo-EM structure of the Bacillus subtilis 100S ribosome,...

Fileemd_3664_additional_1.map
AnnotationCryo-EM structure of the Bacillus subtilis 100S ribosome, filtered final map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the Bacillus subtilis 100S ribosome, half map

Fileemd_3664_half_map_1.map
AnnotationCryo-EM structure of the Bacillus subtilis 100S ribosome, half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the Bacillus subtilis 100S ribosome, half map

Fileemd_3664_half_map_2.map
AnnotationCryo-EM structure of the Bacillus subtilis 100S ribosome, half 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 : Structure of the Bacillus subtilis hibernating 100S ribosome reve...

EntireName: Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.
Components
  • Complex: Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.

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Supramolecule #1: Structure of the Bacillus subtilis hibernating 100S ribosome reve...

SupramoleculeName: Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bacillus subtilis (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: 7.2
VitrificationCryogen name: ETHANE
DetailsStructure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: EMDB MAP
EMDB ID:

3656


Details: previous map calculated and deposited during the previous session D_1200004219
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 19334
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 9.11)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 9.11)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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