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- EMDB-11963: Cryo-EM map of the membrane-associated light-dependent protochlor... -

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Basic information

Entry
Database: EMDB / ID: EMD-11963
TitleCryo-EM map of the membrane-associated light-dependent protochlorophyllide oxidoreductase (LPOR) from Z. mays (subboxed helical arrays, 16 units per turn)
Map data
Sample
  • Organelle or cellular component: membrane-associated light-dependent protochlorophyllide oxidoreductase (LPOR) from Z. mays (subboxed helical arrays, 16 units per turn)
Biological speciesZea mays (maize)
Methodsubtomogram averaging / cryo EM / Resolution: 9.1 Å
AuthorsFloris D / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Plants / Year: 2021
Title: Molecular landscape of etioplast inner membranes in higher plants.
Authors: Davide Floris / Werner Kühlbrandt /
Abstract: Etioplasts are photosynthetically inactive plastids that accumulate when light levels are too low for chloroplast maturation. The etioplast inner membrane consists of a paracrystalline tubular ...Etioplasts are photosynthetically inactive plastids that accumulate when light levels are too low for chloroplast maturation. The etioplast inner membrane consists of a paracrystalline tubular lattice and peripheral, disk-shaped membranes, respectively known as the prolamellar body and prothylakoids. These distinct membrane regions are connected into one continuous compartment. To date, no structures of protein complexes in or at etioplast membranes have been reported. Here, we used electron cryo-tomography to explore the molecular membrane landscape of pea and maize etioplasts. Our tomographic reconstructions show that ATP synthase monomers are enriched in the prothylakoids, and plastid ribosomes in the tubular lattice. The entire tubular lattice is covered by regular helical arrays of a membrane-associated protein, which we identified as the 37-kDa enzyme, light-dependent protochlorophyllide oxidoreductase (LPOR). LPOR is the most abundant protein in the etioplast, where it is responsible for chlorophyll biosynthesis, photoprotection and defining the membrane geometry of the prolamellar body. Based on the 9-Å-resolution volume of the subtomogram average, we propose a structural model of membrane-associated LPOR.
History
DepositionNov 19, 2020-
Header (metadata) releaseApr 21, 2021-
Map releaseApr 21, 2021-
UpdateMay 5, 2021-
Current statusMay 5, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0087
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0087
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11963.png

Downloads & links

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Map

FileDownload / File: emd_11963.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 100 pix.
= 220. Å		2.2 Å/pix.
x 100 pix.
= 220. Å		2.2 Å/pix.
x 100 pix.
= 220. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0087 / Movie #1: 0.0087
Minimum - Maximum-0.016158778 - 0.042208415
Average (Standard dev.)0.00048449094 (±0.005904036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin252525
Dimensions100100100
Spacing100100100
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z220.000220.000220.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS252525
NC/NR/NS100100100
D min/max/mean-0.0160.0420.000

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Supplemental data

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Sample components

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Entire : membrane-associated light-dependent protochlorophyllide oxidoredu...

EntireName: membrane-associated light-dependent protochlorophyllide oxidoreductase (LPOR) from Z. mays (subboxed helical arrays, 16 units per turn)
Components
  • Organelle or cellular component: membrane-associated light-dependent protochlorophyllide oxidoreductase (LPOR) from Z. mays (subboxed helical arrays, 16 units per turn)

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Supramolecule #1: membrane-associated light-dependent protochlorophyllide oxidoredu...

SupramoleculeName: membrane-associated light-dependent protochlorophyllide oxidoreductase (LPOR) from Z. mays (subboxed helical arrays, 16 units per turn)
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Zea mays (maize) / Organelle: etioplast

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

BufferpH: 8
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 20082
ExtractionNumber tomograms: 17 / Number images used: 20082 / Software - Name: Dynamo
CTF correctionSoftware - Name: IMOD
Final angle assignmentType: OTHER
Crystal parametersUnit cell - A: 220 Å / Unit cell - B: 220 Å / Unit cell - C: 220 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: C
FSC plot (resolution estimation)

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