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- EMDB-3942: Structure of the chloroplast ribosome with chl-RRF and hibernatio... -

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Basic information

Entry
Database: EMDB / ID: EMD-3942
TitleStructure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor (Focused refinement of LSU)
Map dataPostprocessed sharpened map that has been resampled onto the map used in the refinement of the coordinates
Sample
  • Complex: Chloroplast ribosome in complex with RRF - Focussed refinement on LSU
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPerez Borema A / Aibara S / Paul B / Tobiasson V / Kimanius D / Forsberg BO / Wallden K / Lindahl E / Amunts A
CitationJournal: Nat Plants / Year: 2018
Title: Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor.
Authors: Annemarie Perez Boerema / Shintaro Aibara / Bijoya Paul / Victor Tobiasson / Dari Kimanius / Björn O Forsberg / Karin Wallden / Erik Lindahl / A Amunts /
Abstract: Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions ...Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast. Chloroplasts evolved ~1.2 billion years ago from an engulfed primordial diazotrophic cyanobacterium, and chlororibosomes are responsible for synthesis of the core proteins driving photochemical reactions. Chlororibosomal activity is spatiotemporally coupled to the synthesis and incorporation of functionally essential co-factors, implying the presence of chloroplast-specific regulatory mechanisms and structural adaptation of the chlororibosome. Despite recent structural information, some of these aspects remained elusive. To provide new insights into the structural specialities and evolution, we report a comprehensive analysis of the 2.9-3.1 Å resolution electron cryo-microscopy structure of the spinach chlororibosome in complex with its recycling factor and hibernation-promoting factor. The model reveals a prominent channel extending from the exit tunnel to the chlororibosome exterior, structural re-arrangements that lead to increased surface area for translocon binding, and experimental evidence for parallel and convergent evolution of chloro- and mitoribosomes.
History
DepositionOct 18, 2017-
Header (metadata) releaseMar 7, 2018-
Map releaseMar 7, 2018-
UpdateApr 18, 2018-
Current statusApr 18, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3942.png

Downloads & links

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Map

FileDownload / File: emd_3942.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed sharpened map that has been resampled onto the map used in the refinement of the coordinates
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 420 pix.
= 445.2 Å		1.06 Å/pix.
x 420 pix.
= 445.2 Å		1.06 Å/pix.
x 420 pix.
= 445.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.19526072 - 0.42300403
Average (Standard dev.)0.00052232825 (±0.009182763)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 445.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z445.200445.200445.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-128-128-128
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.1950.4230.001

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Supplemental data

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Mask #1

Fileemd_3942_msk_1.map
Projections & Slices
AxesZYX

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Additional map: unsharpened map that has been resampled onto the...

Fileemd_3942_additional_1.map
Annotationunsharpened map that has been resampled onto the map used in the refinement of the coordinates
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Postprocessed sharpened map that has not been resampled...

Fileemd_3942_additional_2.map
AnnotationPostprocessed sharpened map that has not been resampled onto the map used in the refinement of the coordinates
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map that has not been resampled onto...

Fileemd_3942_additional_3.map
Annotationunsharpened map that has not been resampled onto the map used in the refinement of the coordinates
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: halfmap 1

Fileemd_3942_half_map_1.map
Annotationhalfmap 1
Projections & Slices
AxesZYX

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Histogram

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Half map: halfmap 2

Fileemd_3942_half_map_2.map
Annotationhalfmap 2
Projections & Slices
AxesZYX

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Sample components

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Entire : Chloroplast ribosome in complex with RRF - Focussed refinement on LSU

EntireName: Chloroplast ribosome in complex with RRF - Focussed refinement on LSU
Components
  • Complex: Chloroplast ribosome in complex with RRF - Focussed refinement on LSU

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Supramolecule #1: Chloroplast ribosome in complex with RRF - Focussed refinement on LSU

SupramoleculeName: Chloroplast ribosome in complex with RRF - Focussed refinement on LSU
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Spinacia oleracea (spinach)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 4.0 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130300
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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