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- EMDB-3825: Three-dimensional cryo-EM density map of paired C2S2M PSII-LHCII ... -

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Basic information

Entry
Database: EMDB / ID: 3825
TitleThree-dimensional cryo-EM density map of paired C2S2M PSII-LHCII supercomplexes from thylakoid membranes of Pisum sativum
Map dataThree-dimensional cryo-EM density map of paired C2S2M PSII-LHCII supercomplexes from thylakoid membranes of Pisum sativum
Samplepaired PSII-LHCII supercomplexes from pea plants:
SourcePisum sativum (pea)
Methodsingle particle reconstruction / cryo EM / 14 Å resolution
AuthorsPagliano C
CitationJournal: Sci Rep / Year: 2017
Title: Pea PSII-LHCII supercomplexes form pairs by making connections across the stromal gap.
Authors: Pascal Albanese / Roberto Melero / Benjamin D Engel / Alessandro Grinzato / Paola Berto / Marcello Manfredi / Angelica Chiodoni / Javier Vargas / Carlos Óscar Sánchez Sorzano / Emilio Marengo / Guido Saracco / Giuseppe Zanotti / Jose-Maria Carazo / Cristina Pagliano
Abstract: In higher plant thylakoids, the heterogeneous distribution of photosynthetic protein complexes is a determinant for the formation of grana, stacks of membrane discs that are densely populated with ...In higher plant thylakoids, the heterogeneous distribution of photosynthetic protein complexes is a determinant for the formation of grana, stacks of membrane discs that are densely populated with Photosystem II (PSII) and its light harvesting complex (LHCII). PSII associates with LHCII to form the PSII-LHCII supercomplex, a crucial component for solar energy conversion. Here, we report a biochemical, structural and functional characterization of pairs of PSII-LHCII supercomplexes, which were isolated under physiologically-relevant cation concentrations. Using single-particle cryo-electron microscopy, we determined the three-dimensional structure of paired CSM PSII-LHCII supercomplexes at 14 Å resolution. The two supercomplexes interact on their stromal sides through a specific overlap between apposing LHCII trimers and via physical connections that span the stromal gap, one of which is likely formed by interactions between the N-terminal loops of two Lhcb4 monomeric LHCII subunits. Fast chlorophyll fluorescence induction analysis showed that paired PSII-LHCII supercomplexes are energetically coupled. Molecular dynamics simulations revealed that additional flexible physical connections may form between the apposing LHCII trimers of paired PSII-LHCII supercomplexes in appressed thylakoid membranes. Our findings provide new insights into how interactions between pairs of PSII-LHCII supercomplexes can link adjacent thylakoids to mediate the stacking of grana membranes.
DateDeposition: Jul 26, 2017 / Header (metadata) release: Aug 30, 2017 / Map release: Sep 6, 2017 / Last update: Sep 20, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0003
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0003
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3825.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.4 Å/pix.
= 560. Å
400 pix
1.4 Å/pix.
= 560. Å
400 pix
1.4 Å/pix.
= 560. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour Level:0.0003 (by author), 0.0003 (movie #1):
Minimum - Maximum-0.0027011025 - 0.022493664
Average (Standard dev.)8.22539E-5 (0.00074280193)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin000
Limit399399399
Spacing400400400
CellA=B=C: 560 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z560.000560.000560.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0030.0220.000

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Supplemental data

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Sample components

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Entire paired PSII-LHCII supercomplexes from pea plants

EntireName: paired PSII-LHCII supercomplexes from pea plants
Details: paired PSII-LHCII supercomplexes connected across the stromal gap
Number of components: 1
MassTheoretical: 2.75 MDa

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Component #1: protein, paired PSII-LHCII supercomplexes from pea plants

ProteinName: paired PSII-LHCII supercomplexes from pea plants
Details: paired PSII-LHCII supercomplexes connected across the stromal gap
Recombinant expression: No
MassTheoretical: 2.75 MDa
SourceSpecies: Pisum sativum (pea) / Strain: Palladio nano
Source (natural)Organelle: Chloroplast / Organ or tissue: Mesophyll

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: fresh solution / pH: 5.7
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 294 K / Humidity: 100 % / Details: blot for 4 seconds befoere plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 7 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 6834

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D2 (2*2 fold dihedral) / Number of projections: 26953
3D reconstructionSoftware: SCIPION / Resolution: 14 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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