Journal: 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 ...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.
History
Deposition
Jul 26, 2017
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Header (metadata) release
Aug 30, 2017
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Map release
Sep 6, 2017
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Update
Sep 20, 2017
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Current status
Sep 20, 2017
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
EMPIAR-10198 (Title: Paired C2S2M PSII-LHCII supercomplexes from thylakoid membranes of Pisum sativum Data size: 433.1 / Data #1: 2.outputMicrographs [micrographs - single frame])
Download / File: emd_3825.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Three-dimensional cryo-EM density map of paired C2S2M PSII-LHCII supercomplexes from thylakoid membranes of Pisum sativum
Voxel size
X=Y=Z: 1.4 Å
Density
Contour Level
By AUTHOR: 0.0003 / Movie #1: 0.0003
Minimum - Maximum
-0.0027011025 - 0.022493664
Average (Standard dev.)
0.0000822539 (±0.00074280193)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
400
400
400
Spacing
400
400
400
Cell
A=B=C: 560.0 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.4
1.4
1.4
M x/y/z
400
400
400
origin x/y/z
0.000
0.000
0.000
length x/y/z
560.000
560.000
560.000
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
400
400
400
D min/max/mean
-0.003
0.022
0.000
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Supplemental data
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Sample components
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Entire : paired PSII-LHCII supercomplexes from pea plants
Entire
Name: paired PSII-LHCII supercomplexes from pea plants
Components
Complex: paired PSII-LHCII supercomplexes from pea plants
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Supramolecule #1: paired PSII-LHCII supercomplexes from pea plants
Supramolecule
Name: paired PSII-LHCII supercomplexes from pea plants / type: complex / ID: 1 / Parent: 0 Details: paired PSII-LHCII supercomplexes connected across the stromal gap
Model: Quantifoil lacey carbon / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE
Vitrification
Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK III / Details: blot for 4 seconds befoere plunging.
Details
Specimen concentration (mg/mL) is given in terms of Chlorophyll
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Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 6834 / Average exposure time: 1.5 sec. / Average electron dose: 7.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics
Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
CTF correction
Software - Name: CTFFIND (ver. 4)
Final reconstruction
Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SCIPION / Number images used: 26953
Initial angle assignment
Type: NOT APPLICABLE
Final angle assignment
Type: NOT APPLICABLE
Final 3D classification
Software - Name: RELION
FSC plot (resolution estimation)
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Atomic model buiding 1
Refinement
Protocol: RIGID BODY FIT
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