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- EMDB-6617: CryoEM map of spinach PSII-LHCII supercomplex at 3.2A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-6617
TitleCryoEM map of spinach PSII-LHCII supercomplex at 3.2A resolution
Map dataA cryo-EM map of a membrane protein complex
Sample
  • Sample: Spinach PSII-LHCII supercomplex
  • Protein or peptide: Photosystem II (or water-plastoquinone oxidoreductase) in complex with Light harvesting complex II
Keywordsmembrane protein / spinach photosystem II / cryo-EM
Function / homology
Function and homology information


chloroplast photosystem II / plastoglobule / : / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center ...chloroplast photosystem II / plastoglobule / : / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / chloroplast envelope / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I / response to herbicide / photosystem II / extrinsic component of membrane / chlorophyll binding / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / : / response to light stimulus / membrane => GO:0016020 / photosynthesis / chloroplast / phosphoprotein binding / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / calcium ion binding / metal ion binding
Similarity search - Function
: / Photosystem II 5kDa protein, chloroplastic / PsbP, C-terminal / PsbP / : / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 ...: / Photosystem II 5kDa protein, chloroplastic / PsbP, C-terminal / PsbP / : / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / 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 reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / 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 cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / 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, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem II 5 kDa protein, chloroplastic / Uncharacterized protein / Chlorophyll a-b binding protein, chloroplastic / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II reaction center protein K ...Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem II 5 kDa protein, chloroplastic / Uncharacterized protein / Chlorophyll a-b binding protein, chloroplastic / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II reaction center protein K / Oxygen-evolving enhancer protein 3, chloroplastic / Oxygen-evolving enhancer protein 2, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Oxygen-evolving enhancer protein 1, chloroplastic / Cytochrome b559 subunit beta / Photosystem II reaction center protein L / Photosystem II reaction center protein T / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Cytochrome b559 subunit alpha / Photosystem II protein D1 / Photosystem II reaction center W protein, chloroplastic / Photosystem II reaction center protein J / Photosystem II reaction center protein Z
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWei XP / Zhang XZ / Su XD / Cao P / Liu XY / Li M / Chang WR / Liu ZF
CitationJournal: Nature / Year: 2016
Title: Structure of spinach photosystem II-LHCII supercomplex at 3.2 Å resolution.
Authors: Xuepeng Wei / Xiaodong Su / Peng Cao / Xiuying Liu / Wenrui Chang / Mei Li / Xinzheng Zhang / Zhenfeng Liu /
Abstract: During photosynthesis, the plant photosystem II core complex receives excitation energy from the peripheral light-harvesting complex II (LHCII). The pathways along which excitation energy is ...During photosynthesis, the plant photosystem II core complex receives excitation energy from the peripheral light-harvesting complex II (LHCII). The pathways along which excitation energy is transferred between them, and their assembly mechanisms, remain to be deciphered through high-resolution structural studies. Here we report the structure of a 1.1-megadalton spinach photosystem II-LHCII supercomplex solved at 3.2 Å resolution through single-particle cryo-electron microscopy. The structure reveals a homodimeric supramolecular system in which each monomer contains 25 protein subunits, 105 chlorophylls, 28 carotenoids and other cofactors. Three extrinsic subunits (PsbO, PsbP and PsbQ), which are essential for optimal oxygen-evolving activity of photosystem II, form a triangular crown that shields the Mn4CaO5-binding domains of CP43 and D1. One major trimeric and two minor monomeric LHCIIs associate with each core-complex monomer, and the antenna-core interactions are reinforced by three small intrinsic subunits (PsbW, PsbH and PsbZ). By analysing the closely connected interfacial chlorophylls, we have obtained detailed insights into the energy-transfer pathways between the antenna and core complexes.
History
DepositionMar 9, 2016-
Header (metadata) releaseMay 11, 2016-
Map releaseMay 25, 2016-
UpdateJun 8, 2016-
Current statusJun 8, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jcu
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6617.gif

Downloads & links

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Map

FileDownload / File: emd_6617.map.gz / Format: CCP4 / Size: 37.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA cryo-EM map of a membrane protein complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 160 pix.
= 216. Å		1.35 Å/pix.
x 250 pix.
= 337.5 Å		1.35 Å/pix.
x 250 pix.
= 337.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.16092882 - 0.39346048
Average (Standard dev.)0.00415091 (±0.02112041)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-125-125-80
Dimensions250250160
Spacing250250160
CellA: 337.5 Å / B: 337.5 Å / C: 216.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z250250160
origin x/y/z0.0000.0000.000
length x/y/z337.500337.500216.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-125-125-80
NC/NR/NS250250160
D min/max/mean-0.1610.3930.004

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Supplemental data

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Sample components

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Entire : Spinach PSII-LHCII supercomplex

EntireName: Spinach PSII-LHCII supercomplex
Components
  • Sample: Spinach PSII-LHCII supercomplex
  • Protein or peptide: Photosystem II (or water-plastoquinone oxidoreductase) in complex with Light harvesting complex II

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Supramolecule #1000: Spinach PSII-LHCII supercomplex

SupramoleculeName: Spinach PSII-LHCII supercomplex / type: sample / ID: 1000 / Oligomeric state: homodimer / Number unique components: 1
Molecular weightExperimental: 1.1 MDa / Theoretical: 1.1 MDa

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Macromolecule #1: Photosystem II (or water-plastoquinone oxidoreductase) in complex...

MacromoleculeName: Photosystem II (or water-plastoquinone oxidoreductase) in complex with Light harvesting complex II
type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Spinacia oleracea (spinach)

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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

Concentration3 mg/mL
GridDetails: 400 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateNov 20, 2015
Image recordingCategory: CCD / Film or detector model: OTHER / Number real images: 1774 / Average electron dose: 50 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: OTHER / Software - Name: EMAN, RELION / Number images used: 109042

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Atomic model buiding 1

Initial modelPDB ID:

4rti

SoftwareName: Chimera, Coot
RefinementSpace: REAL
Output model

PDB-3jcu:
Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angstrom resolution

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Atomic model buiding 2

Initial modelPDB ID:

1vyk

SoftwareName: Phenix
RefinementSpace: REAL
Output model

PDB-3jcu:
Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angstrom resolution

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Atomic model buiding 3

Initial modelPDB ID:

3pl9

SoftwareName: Phenix
RefinementSpace: REAL
Output model

PDB-3jcu:
Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angstrom resolution

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Atomic model buiding 4

Initial modelPDB ID:

1rwt

SoftwareName: Phenix
RefinementSpace: REAL
Output model

PDB-3jcu:
Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angstrom resolution

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