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- EMDB-3491: Cryo-EM structure of the PSII supercomplex from Arabidopsis thaliana -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3491 | |||||||||
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Title | Cryo-EM structure of the PSII supercomplex from Arabidopsis thaliana | |||||||||
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Function / homology | ![]() plastid thylakoid membrane / regulation of protein dephosphorylation / photoinhibition / photosystem II antenna complex / nonphotochemical quenching / sequestering of metal ion / PSII associated light-harvesting complex II / chloroplast stromal thylakoid / thylakoid lumen / thylakoid membrane ...plastid thylakoid membrane / regulation of protein dephosphorylation / photoinhibition / photosystem II antenna complex / nonphotochemical quenching / sequestering of metal ion / PSII associated light-harvesting complex II / chloroplast stromal thylakoid / thylakoid lumen / thylakoid membrane / chloroplast thylakoid / plastoglobule / chloroplast thylakoid lumen / photosystem II assembly / photosynthesis, light harvesting in photosystem I / photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / apoplast / thylakoid / chloroplast envelope / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / photosynthetic electron transport chain / poly(U) RNA binding / response to herbicide / photosystem II / plastid / chlorophyll binding / chloroplast stroma / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / chloroplast thylakoid membrane / response to light stimulus / photosynthetic electron transport in photosystem II / photosynthesis / chloroplast / membrane => GO:0016020 / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / heme binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.3 Å | |||||||||
![]() | van Bezouwen LS / Caffarri S / Kale RS / Kouril R / Thunnissen AMWH / Oostergetel GT / Boekema EJ | |||||||||
![]() | ![]() Title: Subunit and chlorophyll organization of the plant photosystem II supercomplex. Authors: Laura S van Bezouwen / Stefano Caffarri / Ravindra S Kale / Roman Kouřil / Andy-Mark W H Thunnissen / Gert T Oostergetel / Egbert J Boekema / ![]() ![]() ![]() Abstract: Photosystem II (PSII) is a light-driven protein, involved in the primary reactions of photosynthesis. In plant photosynthetic membranes PSII forms large multisubunit supercomplexes, containing a ...Photosystem II (PSII) is a light-driven protein, involved in the primary reactions of photosynthesis. In plant photosynthetic membranes PSII forms large multisubunit supercomplexes, containing a dimeric core and up to four light-harvesting complexes (LHCs), which act as antenna proteins. Here we solved a three-dimensional (3D) structure of the CSM supercomplex from Arabidopsis thaliana using cryo-transmission electron microscopy (cryo-EM) and single-particle analysis at an overall resolution of 5.3 Å. Using a combination of homology modelling and restrained refinement against the cryo-EM map, it was possible to model atomic structures for all antenna complexes and almost all core subunits. We located all 35 chlorophylls of the core region based on the cyanobacterial PSII structure, whose positioning is highly conserved, as well as all the chlorophylls of the LHCII S and M trimers. A total of 13 and 9 chlorophylls were identified in CP26 and CP24, respectively. Energy flow from LHC complexes to the PSII reaction centre is proposed to follow preferential pathways: CP26 and CP29 directly transfer to the core using several routes for efficient transfer; the S trimer is directly connected to CP43 and the M trimer can efficiently transfer energy to the core through CP29 and the S trimer. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 364.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 36.7 KB 36.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.5 KB | Display | ![]() |
Images | ![]() | 91.2 KB | ||
Others | ![]() ![]() | 310.5 MB 310.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 433.8 KB | Display | ![]() |
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Full document | ![]() | 432.9 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mdxMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.105 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_3491_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_3491_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : C2S2M2 supercomplex of Photosystem II
+Supramolecule #1: C2S2M2 supercomplex of Photosystem II
+Macromolecule #1: Photosystem II protein D1
+Macromolecule #2: Photosystem II CP47 reaction center protein
+Macromolecule #3: Photosystem II CP43 reaction center protein
+Macromolecule #4: Photosystem II D2 protein
+Macromolecule #5: Cytochrome b559 subunit alpha
+Macromolecule #6: Cytochrome b559 subunit beta (PsbF)
+Macromolecule #7: Photosystem II reaction center protein H
+Macromolecule #8: Photosystem II reaction center protein I
+Macromolecule #9: Photosystem II reaction center protein K
+Macromolecule #10: Photosystem II reaction center protein L
+Macromolecule #11: Photosystem II reaction center protein M
+Macromolecule #12: Oxygen-evolving enhancer protein 1-1, chloroplastic
+Macromolecule #13: Photosystem II reaction center protein T
+Macromolecule #14: Photosystem II reaction center W protein, chloroplastic
+Macromolecule #15: Photosystem II reaction center protein X
+Macromolecule #16: Photosystem II reaction center protein Z
+Macromolecule #17: Chlorophyll a-b binding protein CP29.1, chloroplastic
+Macromolecule #18: Chlorophyll a-b binding protein CP26, chloroplastic
+Macromolecule #19: Chlorophyll a-b binding protein 1, chloroplastic
+Macromolecule #20: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #21: FE (II) ION
+Macromolecule #22: CHLOROPHYLL A
+Macromolecule #23: PHEOPHYTIN A
+Macromolecule #24: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #25: CHLOROPHYLL B
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Microscope had a Cs corrector |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-7 / Number grids imaged: 3 / Number real images: 5198 / Average exposure time: 1.0 sec. / Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | Initial fitting of the subunits in the cryo-EM map was performed by rigid body real space refinement, using as templates the high resolution crystal structures of Thermosynechococcus vulcanus PSII (PDB code 3WU2), pea LHC-II (PDB code 2BHW for the S- and M-trimers, and spinach CP29 (PDB code 3PL9) for CP29, CP26 and CP24. Local fitting and adjustment of the subunits in the cryo-EM maps was performed using manual rebuilding and restrained real space refinement as explained in the primary reference. Due to large differences in local resolution of the cryo-EM map, refinement of the PSII core, the S-trimer with CP26/CP29 and the M-trimer with CP24 was performed separately in excised parts of the cryo-EM map. The core was refined at 4.5 angstrom, the S-trimer+CP26+CP29 at 5.5 angstrom and the M-trimer+CP24 at 6.5 angstrom. Core: chains A,B,C,D,E,F,H,I,J,K,L,M,O,T,W,X,Z and a,b,c,d,e,f,h,i,j,k,l,m,o,t,w,x,z. S-trimer+CP26+CP29: chains G,N,Y,S,R and g,n,y,s,r. M-trimer+CP24: chains 1,2,3,4 and 5,6,7,8. |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient |
Output model | ![]() PDB-5mdx: |