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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: EMD-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
Sample
  • Complex: paired PSII-LHCII supercomplexes from pea plants
Biological speciesPisum sativum (garden pea)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
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 ...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
DepositionJul 26, 2017-
Header (metadata) releaseAug 30, 2017-
Map releaseSep 6, 2017-
UpdateSep 20, 2017-
Current statusSep 20, 2017Processing site: PDBe / Status: Released

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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

emd_3825.png

Downloads & links

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Map

FileDownload / File: emd_3825.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThree-dimensional cryo-EM density map of paired C2S2M PSII-LHCII supercomplexes from thylakoid membranes of Pisum sativum
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0003 / Movie #1: 0.0003
Minimum - Maximum-0.0027011025 - 0.022493664
Average (Standard dev.)0.0000822539 (±0.00074280193)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 560.0 Å
α=β=γ: 90.0 °

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
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
Components
  • Complex: paired PSII-LHCII supercomplexes from pea plants

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Supramolecule #1: paired PSII-LHCII supercomplexes from pea plants

SupramoleculeName: paired PSII-LHCII supercomplexes from pea plants / type: complex / ID: 1 / Parent: 0
Details: paired PSII-LHCII supercomplexes connected across the stromal gap
Source (natural)Organism: Pisum sativum (garden pea) / Strain: Palladio nano
Molecular weightTheoretical: 2.75 MDa

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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

Concentration1 mg/mL
BufferpH: 5.7 / Component - Concentration: 25.0 mM / Component - Formula: C6H13NO4S / Component - Name: MES / Details: fresh solution
GridModel: Quantifoil lacey carbon / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK III / Details: blot for 4 seconds befoere plunging.
DetailsSpecimen concentration (mg/mL) is given in terms of Chlorophyll

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 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)
Final reconstructionApplied 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 assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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