- EMDB-3491: Cryo-EM structure of the PSII supercomplex from Arabidopsis thaliana -
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Basic information
Entry
Database: EMDB / ID: EMD-3491
Title
Cryo-EM structure of the PSII supercomplex from Arabidopsis thaliana
Map data
Sample
Complex: C2S2M2 supercomplex of Photosystem II
Protein or peptide: x 20 types
Ligand: x 5 types
Function / homology
Function and homology information
plastid thylakoid membrane / regulation of protein dephosphorylation / photoinhibition / photosystem II antenna complex / PSII associated light-harvesting complex II / nonphotochemical quenching / sequestering of metal ion / chloroplast stromal thylakoid / thylakoid lumen / plastoglobule ...plastid thylakoid membrane / regulation of protein dephosphorylation / photoinhibition / photosystem II antenna complex / PSII associated light-harvesting complex II / nonphotochemical quenching / sequestering of metal ion / chloroplast stromal thylakoid / thylakoid lumen / plastoglobule / thylakoid membrane / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / apoplast / photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / chloroplast envelope / thylakoid / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / poly(U) RNA binding / response to herbicide / photosystem II / plastid / chloroplast stroma / photosynthetic electron transport in photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / response to light stimulus / photosynthesis / chloroplast / electron transfer activity / membrane => GO:0016020 / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / heme binding / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function
Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM ...Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. Similarity search - Domain/homology
Chlorophyll a-b binding protein 1, chloroplastic / Oxygen-evolving enhancer protein 1-1, chloroplastic / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II reaction center protein Z / Photosystem II reaction center protein L ...Chlorophyll a-b binding protein 1, chloroplastic / Oxygen-evolving enhancer protein 1-1, chloroplastic / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II reaction center protein Z / Photosystem II reaction center protein L / Photosystem II reaction center protein T / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Photosystem II protein D1 / Chlorophyll a-b binding protein CP29.1, chloroplastic / Photosystem II reaction center W protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Expressed protein / Chlorophyll a-b binding protein CP26, chloroplastic Similarity search - Component
Journal: Nat Plants / Year: 2017 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
Deposition
Nov 13, 2016
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Header (metadata) release
Jun 21, 2017
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Map release
Jun 21, 2017
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Update
Apr 24, 2019
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Current status
Apr 24, 2019
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
CTF correction
Software - Name: RELION (ver. 1.3)
Startup model
Type of model: OTHER / Details: The RANSAC method is used (Vargas 2014)
Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 23434
FSC plot (resolution estimation)
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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.
Refinement
Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model
PDB-5mdx: Cryo-EM structure of the PSII supercomplex from Arabidopsis thaliana
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Open data
Basic information
Map data
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Function and homology information
photoinhibition / 
Authors
Citation
Structure visualization
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emd_3491.png
http://ftp.pdbj.org/pub/emdb/structures/EMD-3491
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Sample components
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Electron microscopy
