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Yorodumi- EMDB-3825: Three-dimensional cryo-EM density map of paired C2S2M PSII-LHCII ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3825 | |||||||||
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Title | Three-dimensional cryo-EM density map of paired C2S2M PSII-LHCII supercomplexes from thylakoid membranes of Pisum sativum | |||||||||
Map data | Three-dimensional cryo-EM density map of paired C2S2M PSII-LHCII supercomplexes from thylakoid membranes of Pisum sativum | |||||||||
Sample |
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Biological species | Pisum sativum (garden pea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.0 Å | |||||||||
Authors | Pagliano C | |||||||||
Citation | 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3825.map.gz | 235.8 MB | EMDB map data format | |
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Header (meta data) | emd-3825-v30.xml emd-3825.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3825_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_3825.png | 65.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3825 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3825 | HTTPS FTP |
-Related structure data
Similar structure data | |
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EM raw data | 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]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3825.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : paired PSII-LHCII supercomplexes from pea plants
Entire | Name: paired PSII-LHCII supercomplexes from pea plants |
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Components |
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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 |
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Source (natural) | Organism: Pisum sativum (garden pea) / Strain: Palladio nano |
Molecular weight | Theoretical: 2.75 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 5.7 / Component - Concentration: 25.0 mM / Component - Formula: C6H13NO4S / Component - Name: MES / Details: fresh solution |
Grid | 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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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