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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
SampleM-LHCII and CP24 complexes in the stacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
SourcePisum sativum / plant / peas / エンドウ
Map dataNone
Methodsingle particle reconstruction, at 3.6 Å resolution
AuthorsSu XD / Ma J / Wei XP / Cao P / Zhu DJ / Chang WR / Liu ZF / Zhang XZ / Li M
CitationScience, 2017, 357, 815-820

Science, 2017, 357, 815-820 Yorodumi Papers
Structure and assembly mechanism of plant C2S2M2-type PSII-LHCII supercomplex.
Xiaodong Su / Jun Ma / Xuepeng Wei / Peng Cao / Dongjie Zhu / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li

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
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  • Surface view with fitted model
  • Atomic models: : PDB-5xnn
  • Surface level: 0.028
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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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 package.

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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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

Specimen stateparticle
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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