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

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Basic information

Entry
Database: EMDB / ID: 6742
TitleStructure of unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
SampleC2S2M2-type PSII-LHCII supercomplex from Pisum sativum
SourcePisum sativum / plant / peas / エンドウ
Map data
Methodsingle particle reconstruction, at 3.2 Å resolution
AuthorsSu XD / Ma J
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: 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
3D viewer


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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 package.

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 / 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: protein, Photosystem II protein D1

ProteinName: Photosystem II protein D1 / Recombinant expression: No
MassTheoretical: 38.14743 kDa
SourceSpecies: Pisum sativum / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 / plant / peas / エンドウ

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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 ION / 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

Specimen stateparticle
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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