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- EMDB-6743: Structure of M-LHCII and CP24 complexes in the stacked C2S2M2-typ... -

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Basic information

Entry
Database: EMDB / ID: 6743
TitleStructure of M-LHCII and CP24 complexes in the stacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
Map data
SampleM-LHCII and CP24 complexes in the stacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
  • (Chlorophyll a-b binding ...) x 2
  • Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24
  • (ligand) x 7
Function / homologyChlorophyll A-B binding protein, plant / Chlorophyll A-B binding protein / Chlorophyll a/b binding domain superfamily / Chlorophyll A-B binding protein / photosynthesis, light harvesting / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / protein-chromophore linkage ...Chlorophyll A-B binding protein, plant / Chlorophyll A-B binding protein / Chlorophyll a/b binding domain superfamily / Chlorophyll A-B binding protein / photosynthesis, light harvesting / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / protein-chromophore linkage / integral component of membrane / metal ion binding / Chlorophyll a-b binding protein 8, chloroplastic / Chlorophyll a-b binding protein, chloroplastic
Function and homology information
SourcePisum sativum (pea)
Methodsingle particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsSu XD / Ma J / Wei XP / Cao P / Zhu DJ / Chang WR / Liu ZF / Zhang XZ / Li M
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: 5xnn

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: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5xnn
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6743.map.gz (map file in CCP4 format, 13501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
150 pix
1.04 Å/pix.
= 156. Å
150 pix
1.04 Å/pix.
= 156. Å
150 pix
1.04 Å/pix.
= 156. 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:0.028 (by author), 0.028 (movie #1):
Minimum - Maximum-0.08030502 - 0.112424865
Average (Standard dev.)0.00075674115 (0.0074199056)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions150150150
Origin-75-75-75
Limit747474
Spacing150150150
CellA=B=C: 156 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z156.000156.000156.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-75-75-75
NC/NR/NS150150150
D min/max/mean-0.0800.1120.001

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Supplemental data

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Sample components

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Entire M-LHCII and CP24 complexes in the stacked C2S2M2-type PSII-LHCII ...

EntireName: M-LHCII and CP24 complexes in the stacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
Number of components: 11

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Component #1: protein, M-LHCII and CP24 complexes in the stacked C2S2M2-type PS...

ProteinName: M-LHCII and CP24 complexes in the stacked 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: ligand, CHLOROPHYLL B

LigandName: CHLOROPHYLL B / Number of Copies: 23 / Recombinant expression: No
MassTheoretical: 0.907472 kDa

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Component #6: ligand, CHLOROPHYLL A

LigandName: CHLOROPHYLL A / Number of Copies: 30 / Recombinant expression: No
MassTheoretical: 0.893489 kDa

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Component #7: 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: 7 / Recombinant expression: No
MassTheoretical: 0.568871 kDa

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Component #8: 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: 4 / Recombinant expression: No
MassTheoretical: 0.60087 kDa

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Component #9: 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: 3 / Recombinant expression: No
MassTheoretical: 0.60087 kDa

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Component #10: ligand, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

LigandName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.72297 kDa

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Component #11: ligand, BETA-CAROTENE

LigandName: BETA-CAROTENE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.536873 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: 5.7
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: C1 (asymmetric) / Number of projections: 136521
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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