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- EMDB-9680: Photosystem I of Chlamydomonas reinhardtii -

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Basic information

Entry
Database: EMDB / Id: 9680
TitlePhotosystem I of Chlamydomonas reinhardtii
Map data
SampleChlamydomonas reinhardtii PSI with ten light harvesting antennae:
PsaA / PsaB / PsaC / PsaD / PsaE / PsaF / PsaG / PsaH / PsaI / PsaJ ...PsaA / PsaB / PsaC / PsaD / PsaE / PsaF / PsaG / PsaH / PsaI / PsaJ / PsaK / PsaL / Lhca1 / Lhca3 / Lhca4 / Lhca5 / Lhca6 / Lhca7 / Lhca8 / Lhca2 / Lhca9 / ChainX / (ligand) x 11
SourceChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPan X / Ma J / Su X / Liu Z / Zhang X / Li M
CitationJournal: Nat Plants / Year: 2019
Title: Antenna arrangement and energy transfer pathways of a green algal photosystem-I-LHCI supercomplex.
P-authors: Xiaodong Su / Jun Ma / Xiaowei Pan / Xuelin Zhao / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li /
Abstract: During oxygenic photosynthesis, photosystems I and II (PSI and PSII) are essential for light-driven electron transport. Excitation energy transfer in PSI occurs extremely quickly, making it an ...During oxygenic photosynthesis, photosystems I and II (PSI and PSII) are essential for light-driven electron transport. Excitation energy transfer in PSI occurs extremely quickly, making it an efficient energy converter. In the alga Chlamydomonas reinhardtii (Cr), multiple units of light-harvesting complex I (LHCI) bind to the PSI core and function as peripheral antennae, forming a PSI-LHCI supercomplex. CrPSI-LHCI shows significantly larger antennae compared with plant PSI-LHCI while maintaining highly efficient energy transfer from LHCI to PSI. Here, we report structures of CrPSI-LHCI, solved by cryo-electron microscopy, revealing that up to ten LHCIs are associated with the PSI core. The structures provide detailed information about antenna organization and pigment arrangement within the supercomplexes. Highly populated and closely associated chlorophylls in the antennae explain the high efficiency of light harvesting and excitation energy transfer in CrPSI-LHCI.
Validation ReportPDB-ID: 6ijo

SummaryFull reportAbout validation report
DateDeposition: Oct 10, 2018 / Header (metadata) release: Jun 20, 2018 / Map release: Jun 20, 2018 / Last update: Mar 27, 2019

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Strvis

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ijo
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downlink

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Map

Fileemd_9680.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.04 Å/pix.
= 208. Å
200 pix
1.04 Å/pix.
= 208. Å
200 pix
1.04 Å/pix.
= 208. 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:0.06 (by author), 0.06 (movie #1):
Minimum - Maximum-0.13506502 - 0.40000448
Average (Standard dev.)0.0039162426 (0.022058094)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin-100.0-100.0-100.0
Limit99.099.099.0
Spacing200200200
CellA=B=C: 208.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z208.000208.000208.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.1350.4000.004

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Supplemental data

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Sample components

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Entire Chlamydomonas reinhardtii PSI with ten light harvesting antennae

EntireName: Chlamydomonas reinhardtii PSI with ten light harvesting antennae
Number of components: 34

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Component #1: protein, Chlamydomonas reinhardtii PSI with ten light harvesting ...

ProteinName: Chlamydomonas reinhardtii PSI with ten light harvesting antennae
Recombinant expression: No
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #2: protein, PsaA

ProteinName: PsaA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 83.239203 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #3: protein, PsaB

ProteinName: PsaB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 82.184266 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #4: protein, PsaC

ProteinName: PsaC / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.869325 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #5: protein, PsaD

ProteinName: PsaD / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.298189 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #6: protein, PsaE

ProteinName: PsaE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.221703 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #7: protein, PsaF

ProteinName: PsaF / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.088936 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #8: protein, PsaG

ProteinName: PsaG / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.720939 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #9: protein, PsaH

ProteinName: PsaH / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.097596 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #10: protein, PsaI

ProteinName: PsaI / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.586388 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #11: protein, PsaJ

ProteinName: PsaJ / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.750509 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #12: protein, PsaK

ProteinName: PsaK / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.412221 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #13: protein, PsaL

ProteinName: PsaL / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.203562 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #14: protein, Lhca1

ProteinName: Lhca1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.135863 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #15: protein, Lhca3

ProteinName: Lhca3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.629486 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #16: protein, Lhca4

ProteinName: Lhca4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.46201 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #17: protein, Lhca5

ProteinName: Lhca5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.15165 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #18: protein, Lhca6

ProteinName: Lhca6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.122043 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #19: protein, Lhca7

ProteinName: Lhca7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.248869 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #20: protein, Lhca8

ProteinName: Lhca8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.178635 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #21: protein, Lhca2

ProteinName: Lhca2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.947777 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #22: protein, Lhca9

ProteinName: Lhca9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.867277 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #23: protein, ChainX

ProteinName: ChainX / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.866038 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #24: ligand, CHLOROPHYLL A

LigandName: CHLOROPHYLL A / Number of Copies: 243 / Recombinant expression: No
MassTheoretical: 0.893489 kDa

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Component #25: ligand, PHYLLOQUINONE

LigandName: PHYLLOQUINONEPhytomenadione / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.450696 kDa

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Component #26: ligand, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

LigandName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 0.72297 kDa

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Component #27: ligand, BETA-CAROTENE

LigandName: BETA-CAROTENE / Number of Copies: 31 / Recombinant expression: No
MassTheoretical: 0.536873 kDa

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Component #28: ligand, DODECYL-ALPHA-D-MALTOSIDE

LigandName: DODECYL-ALPHA-D-MALTOSIDE / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 0.510615 kDa

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Component #29: ligand, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

LigandName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 0.787158 kDa

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Component #30: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Component #31: ligand, DIGALACTOSYL DIACYL GLYCEROL (DGDG)

LigandName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.949299 kDa

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Component #32: 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: 10 / Recombinant expression: No
MassTheoretical: 0.568871 kDa

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Component #33: 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: 10 / Recombinant expression: No
MassTheoretical: 0.60087 kDa

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Component #34: 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: 2 / Recombinant expression: No
MassTheoretical: 0.60087 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionPh: 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 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 17420
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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