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- EMDB-6742: Structure of unstacked C2S2M2-type PSII-LHCII supercomplex from P... -

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Entry
Database: EMDB / ID: 6742
TitleStructure of unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
Map data
SampleC2S2M2-type PSII-LHCII supercomplex from Pisum sativum
  • (Chlorophyll a-b binding ...) x 2
  • (Light harvesting chlorophyll a/b-binding protein ...) x 3
  • (Photosystem II ...) x 15
  • (Cytochrome b559 subunit ...) x 2
  • Oxygen-evolving enhancer protein 1, chloroplastic
  • (ligand) x 16
Function / homologyPhotosystem II PsbX, type 1 subfamily / Photosystem II PsbX / Photosystem II PsbJ / Photosystem II PsbL / Photosystem II PsbI / Photosystem II PsbK / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II CP43 reaction centre protein / Photosystem II cytochrome b559, conserved site ...Photosystem II PsbX, type 1 subfamily / Photosystem II PsbX / Photosystem II PsbJ / Photosystem II PsbL / Photosystem II PsbI / Photosystem II PsbK / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II CP43 reaction centre protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II PsbM / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosystem II PsbT superfamily / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II CP47 reaction centre protein / Chlorophyll A-B binding protein / Chlorophyll a/b binding domain superfamily / Photosystem antenna protein-like superfamily / Photosystem II PsbZ superfamily / Photosystem II protein D1/D2 superfamily / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Photosystem II PsbL superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbO, manganese-stabilising / Photosystem II PsbT / Chlorophyll A-B binding protein, plant / Cytochrome b559 subunits heme-binding site signature. / Photosynthetic reaction center proteins signature. / Photosystem II reaction centre X protein (PsbX) / Photosystem II reaction centre M protein (PsbM) / Photosystem II 4 kDa reaction centre component / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / PsbL protein / PsbJ / YCF9 / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre T protein / Photosystem II 10 kDa phosphoprotein / Chlorophyll A-B binding protein / Photosystem II protein / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Photosynthetic reaction centre protein / Photosystem II PsbI superfamily / Photosystem II PsbK superfamily / Photosystem II PsbM superfamily / Photosynthetic reaction centre, L/M / Photosystem antenna protein-like / Photosystem II reaction centre protein H / Photosystem II PsbJ superfamily / photosynthesis, light harvesting / photosystem I / photosystem II / photosystem II reaction center / oxygen evolving activity / photosystem II stabilization / photosystem II assembly / photosystem II oxygen evolving complex / photosystem II / chlorophyll binding / photosynthetic electron transport chain / response to herbicide / phosphate ion binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / chloroplast thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / protein-chromophore linkage / protein stabilization / heme binding / integral component of membrane / metal ion binding / Photosystem II reaction center protein H / Ultraviolet-B-repressible protein / Photosystem II reaction center protein T / Photosystem II reaction center protein Z / Chlorophyll a-b binding protein, chloroplastic / Photosystem II reaction center protein M / Cytochrome b559 subunit beta / Photosystem II reaction center protein L / Oxygen-evolving enhancer protein 1, chloroplastic / Chlorophyll a-b binding protein 8, chloroplastic / Photosystem II reaction center protein J / Cytochrome b559 subunit alpha / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein I / Photosystem II reaction center protein K / Uncharacterized protein / Photosystem II CP47 reaction center protein
Function and homology information
SourcePisum sativum (pea)
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsSu XD / Ma J
CitationJournal: Science / Year: 2017
Title: Structure and assembly mechanism of plant CSM-type PSII-LHCII supercomplex.
Authors: Xiaodong Su / Jun Ma / Xuepeng Wei / Peng Cao / Dongjie Zhu / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li
Abstract: In plants, the photosynthetic machinery photosystem II (PSII) consists of a core complex associated with variable numbers of light-harvesting complexes II (LHCIIs). The supercomplex, comprising a ...In plants, the photosynthetic machinery photosystem II (PSII) consists of a core complex associated with variable numbers of light-harvesting complexes II (LHCIIs). The supercomplex, comprising a dimeric core and two strongly bound and two moderately bound LHCIIs (CSM), is the dominant form in plants acclimated to limited light. Here we report cryo-electron microscopy structures of two forms of CSM (termed stacked and unstacked) from at 2.7- and 3.2-angstrom resolution, respectively. In each CSM, the moderately bound LHCII assembles specifically with a peripheral antenna complex CP24-CP29 heterodimer and the strongly bound LHCII, to establish a pigment network that facilitates light harvesting at the periphery and energy transfer into the core. The high mobility of peripheral antennae, including the moderately bound LHCII and CP24, provides insights into functional regulation of plant PSII.
Validation ReportPDB-ID: 5xnm

SummaryFull reportAbout validation report
DateDeposition: May 23, 2017 / Header (metadata) release: Sep 27, 2017 / Map release: Sep 27, 2017 / Last update: Sep 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5xnm
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6742.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.04 Å/pix.
= 312. Å
300 pix
1.04 Å/pix.
= 312. Å
300 pix
1.04 Å/pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour Level:0.026 (by author), 0.026 (movie #1):
Minimum - Maximum-0.057511434 - 0.11831094
Average (Standard dev.)0.00011920636 (0.0067757596)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin-150-150-150
Limit149149149
Spacing300300300
CellA=B=C: 312 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-0.0580.1180.000

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Supplemental data

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Sample components

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Entire C2S2M2-type PSII-LHCII supercomplex from Pisum sativum

EntireName: C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
Number of components: 40

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Component #1: protein, C2S2M2-type PSII-LHCII supercomplex from Pisum sativum

ProteinName: C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
Recombinant expression: No
SourceSpecies: Pisum sativum (pea)

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Component #2: protein, Chlorophyll a-b binding protein 8, chloroplastic

ProteinName: Chlorophyll a-b binding protein 8, chloroplastic / Recombinant expression: No
MassTheoretical: 24.952113 kDa
SourceSpecies: Pisum sativum (pea)

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Component #3: protein, Chlorophyll a-b binding protein, chloroplastic

ProteinName: Chlorophyll a-b binding protein, chloroplastic / Recombinant expression: No
MassTheoretical: 26.54524 kDa
SourceSpecies: Pisum sativum (pea)

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Component #4: protein, Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24

ProteinName: Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24
Recombinant expression: No
MassTheoretical: 22.858957 kDa
SourceSpecies: Pisum sativum (pea)

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Component #5: protein, Photosystem II protein D1

ProteinName: Photosystem II protein D1 / Recombinant expression: No
MassTheoretical: 38.14743 kDa
SourceSpecies: Pisum sativum (pea)

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Component #6: protein, Photosystem II CP47 reaction center protein

ProteinName: Photosystem II CP47 reaction center protein / Recombinant expression: No
MassTheoretical: 56.11784 kDa
SourceSpecies: Pisum sativum (pea)

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Component #7: protein, Photosystem II CP43 reaction center protein

ProteinName: Photosystem II CP43 reaction center protein / Recombinant expression: No
MassTheoretical: 52.035629 kDa
SourceSpecies: Pisum sativum (pea)

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Component #8: protein, Photosystem II D2 protein

ProteinName: Photosystem II D2 protein / Recombinant expression: No
MassTheoretical: 39.557199 kDa
SourceSpecies: Pisum sativum (pea)

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Component #9: protein, Cytochrome b559 subunit alpha

ProteinName: Cytochrome b559 subunit alpha / Recombinant expression: No
MassTheoretical: 9.421555 kDa
SourceSpecies: Pisum sativum (pea)

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Component #10: protein, Cytochrome b559 subunit beta, PsbF

ProteinName: Cytochrome b559 subunit beta, PsbF / Recombinant expression: No
MassTheoretical: 4.488324 kDa
SourceSpecies: Pisum sativum (pea)

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Component #11: protein, Photosystem II reaction center protein H

ProteinName: Photosystem II reaction center protein H / Recombinant expression: No
MassTheoretical: 7.863094 kDa
SourceSpecies: Pisum sativum (pea)

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Component #12: protein, Photosystem II reaction center protein I, PsbI

ProteinName: Photosystem II reaction center protein I, PsbI / Recombinant expression: No
MassTheoretical: 4.184918 kDa
SourceSpecies: Pisum sativum (pea)

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Component #13: protein, Photosystem II reaction center protein J

ProteinName: Photosystem II reaction center protein J / Recombinant expression: No
MassTheoretical: 4.116847 kDa
SourceSpecies: Pisum sativum (pea)

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Component #14: protein, Photosystem II reaction center protein K

ProteinName: Photosystem II reaction center protein K / Recombinant expression: No
MassTheoretical: 6.91229 kDa
SourceSpecies: Pisum sativum (pea)

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Component #15: protein, Photosystem II reaction center protein L

ProteinName: Photosystem II reaction center protein L / Recombinant expression: No
MassTheoretical: 4.4981 kDa
SourceSpecies: Pisum sativum (pea)

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Component #16: protein, Photosystem II reaction center protein M

ProteinName: Photosystem II reaction center protein M / Recombinant expression: No
MassTheoretical: 3.756513 kDa
SourceSpecies: Pisum sativum (pea)

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Component #17: protein, Oxygen-evolving enhancer protein 1, chloroplastic

ProteinName: Oxygen-evolving enhancer protein 1, chloroplastic / Recombinant expression: No
MassTheoretical: 26.554646 kDa
SourceSpecies: Pisum sativum (pea)

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Component #18: protein, Light harvesting chlorophyll a/b-binding protein Lhcb4, CP29

ProteinName: Light harvesting chlorophyll a/b-binding protein Lhcb4, CP29
Recombinant expression: No
MassTheoretical: 27.138688 kDa
SourceSpecies: Pisum sativum (pea)

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Component #19: protein, Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26

ProteinName: Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26
Recombinant expression: No
MassTheoretical: 26.541545 kDa
SourceSpecies: Pisum sativum (pea)

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Component #20: protein, Photosystem II reaction center protein T

ProteinName: Photosystem II reaction center protein T / Recombinant expression: No
MassTheoretical: 4.036859 kDa
SourceSpecies: Pisum sativum (pea)

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Component #21: protein, Photosystem II luminal extrinsic protein Tn, PsbTn

ProteinName: Photosystem II luminal extrinsic protein Tn, PsbTn / Recombinant expression: No
MassTheoretical: 10.676572 kDa
SourceSpecies: Pisum sativum (pea)

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Component #22: protein, Photosystem II reaction center protein W, PSBW

ProteinName: Photosystem II reaction center protein W, PSBW / Recombinant expression: No
MassTheoretical: 5.914629 kDa
SourceSpecies: Pisum sativum (pea)

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Component #23: protein, Photosystem II reaction center protein X

ProteinName: Photosystem II reaction center protein X / Recombinant expression: No
MassTheoretical: 8.692072 kDa
SourceSpecies: Pisum sativum (pea)

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Component #24: protein, Photosystem II reaction center protein Z

ProteinName: Photosystem II reaction center protein Z / Recombinant expression: No
MassTheoretical: 6.555742 kDa
SourceSpecies: Pisum sativum (pea)

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Component #25: ligand, CHLOROPHYLL B

LigandName: CHLOROPHYLL B / Number of Copies: 98 / Recombinant expression: No
MassTheoretical: 0.907472 kDa

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Component #26: ligand, CHLOROPHYLL A

LigandName: CHLOROPHYLL A / Number of Copies: 216 / Recombinant expression: No
MassTheoretical: 0.893489 kDa

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Component #27: ligand, (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-...

LigandName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
Number of Copies: 32 / Recombinant expression: No
MassTheoretical: 0.568871 kDa

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Component #28: ligand, (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRA...

LigandName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 0.60087 kDa

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Component #29: ligand, (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4...

LigandName: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 0.60087 kDa

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Component #30: ligand, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

LigandName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Number of Copies: 36 / Recombinant expression: No
MassTheoretical: 0.72297 kDa

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Component #31: ligand, BETA-CAROTENE

LigandName: BETA-CAROTENE / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 0.536873 kDa

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Component #32: ligand, CA-MN4-O5 CLUSTER

LigandName: CA-MN4-O5 CLUSTER / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.339827 kDa

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Component #33: ligand, FE (II) ION

LigandName: FE (II) ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 5.584505 MDa

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Component #34: ligand, PHEOPHYTIN A

LigandName: PHEOPHYTIN A / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.8712 kDa

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Component #35: ligand, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL...

LigandName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.795116 kDa

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Component #36: ligand, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

LigandName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Number of Copies: 14 / Recombinant expression: No
MassTheoretical: 0.787158 kDa

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Component #37: ligand, 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,1...

LigandName: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.749201 kDa

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Component #38: ligand, DIGALACTOSYL DIACYL GLYCEROL (DGDG)

LigandName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 0.949299 kDa

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Component #39: ligand, BICARBONATE ION

LigandName: BICARBONATE IONBicarbonate / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.101705 MDa

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Component #40: ligand, PROTOPORPHYRIN IX CONTAINING FE

LigandName: PROTOPORPHYRIN IX CONTAINING FE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.616487 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/ml / pH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 50237
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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