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- PDB-6ijo: Photosystem I of Chlamydomonas reinhardtii -

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Entry
Database: PDB / ID: 6ijo
TitlePhotosystem I of Chlamydomonas reinhardtii
Components
  • ChainX
  • Lhca1
  • Lhca2
  • Lhca3
  • Lhca4
  • Lhca5
  • Lhca6
  • Lhca7
  • Lhca8
  • Lhca9
  • PsaA
  • PsaB
  • PsaC
  • PsaD
  • PsaE
  • PsaF
  • PsaG
  • PsaH
  • PsaI
  • PsaJ
  • PsaK
  • PsaL
KeywordsPHOTOSYNTHESIS / Photosystem / Antenna / Supercomplex / green alga
Specimen sourceChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPan, X. / Ma, J. / Su, X. / Liu, Z. / Zhang, X. / Li, M.
Funding supportChina , 10 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFA0503702China
Ministry of Science and Technology (China)2017YFA0504700China
Ministry of Science and Technology (China)2016YFA0502900China
Chinese Academy of SciencesXDB08020302China
Chinese Academy of SciencesXDB08030204China
Chinese Academy of SciencesXDB27020106China
Chinese Academy of SciencesQYZDB-SSW-SMC005China
National Natural Science Foundation of China31770778China
National Natural Science Foundation of China31700649China
National Natural Science Foundation of China31600609China
CitationJournal: Nat Plants / Year: 2019
Title: Antenna arrangement and energy transfer pathways of a green algal photosystem-I-LHCI supercomplex.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Oct 10, 2018 / Release: Mar 20, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 20, 2019Structure modelrepositoryInitial release
1.1Mar 27, 2019Structure modelData collection / Database references / Structure summarycitation / citation_author / struct_struct.title

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Structure visualization

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Assembly

Deposited unit
A: PsaA
B: PsaB
C: PsaC
D: PsaD
E: PsaE
F: PsaF
G: PsaG
H: PsaH
I: PsaI
J: PsaJ
K: PsaK
L: PsaL
1: Lhca1
a: Lhca1
3: Lhca3
4: Lhca4
5: Lhca5
6: Lhca6
7: Lhca7
8: Lhca8
2: Lhca2
9: Lhca9
X: ChainX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)892,585356
Polyers621,41823
Non-polymers271,167333
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 22 types, 23 molecules ABCDEFGHIJKL1a34567829X

#1: Protein/peptide PsaA


Mass: 83239.203 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#2: Protein/peptide PsaB


Mass: 82184.266 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#3: Protein/peptide PsaC


Mass: 8869.325 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#4: Protein/peptide PsaD


Mass: 27298.189 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#5: Protein/peptide PsaE


Mass: 16221.703 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#6: Protein/peptide PsaF


Mass: 24088.936 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#7: Protein/peptide PsaG


Mass: 16720.939 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#8: Protein/peptide PsaH


Mass: 17097.596 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#9: Protein/peptide PsaI


Mass: 10586.388 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#10: Protein/peptide PsaJ


Mass: 4750.509 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#11: Protein/peptide PsaK


Mass: 16412.221 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#12: Protein/peptide PsaL


Mass: 27203.562 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#13: Protein/peptide Lhca1


Mass: 26135.863 Da / Num. of mol.: 2 / Source: (natural) Chlamydomonas reinhardtii (plant)
#14: Protein/peptide Lhca3


Mass: 32629.486 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#15: Protein/peptide Lhca4


Mass: 31462.010 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#16: Protein/peptide Lhca5


Mass: 30151.650 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#17: Protein/peptide Lhca6


Mass: 35122.043 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#18: Protein/peptide Lhca7


Mass: 26248.869 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#19: Protein/peptide Lhca8


Mass: 29178.635 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#20: Protein/peptide Lhca2


Mass: 24947.777 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#21: Protein/peptide Lhca9


Mass: 22867.277 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)
#22: Protein/peptide ChainX


Mass: 1866.038 Da / Num. of mol.: 1 / Source: (natural) Chlamydomonas reinhardtii (plant)

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Non-polymers , 11 types, 333 molecules

#23: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 243 / Formula: C55H72MgN4O5 / Chlorophyll a
#24: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Formula: C31H46O2 / Phytomenadione
#25: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 16 / Formula: C38H75O10P
#26: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 31 / Formula: C40H56 / Beta-Carotene
#27: Chemical
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Mass: 510.615 Da / Num. of mol.: 7 / Formula: C24H46O11 / Comment: detergent *YM
#28: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 7 / Formula: C45H86O10
#29: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Formula: Fe4S4 / Iron–sulfur cluster
#30: Chemical ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Mass: 949.299 Da / Num. of mol.: 2 / Formula: C51H96O15
#31: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL, LUTEIN


Mass: 568.871 Da / Num. of mol.: 10 / Formula: C40H56O2 / Lutein
#32: Chemical
ChemComp-XAT / (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 / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 10 / Formula: C40H56O4 / Violaxanthin
#33: Chemical ChemComp-NEX / (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 / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL, 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 2 / Formula: C40H56O4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Chlamydomonas reinhardtii PSI with ten light harvesting antennae
Type: COMPLEX
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
Source: NATURAL
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17420 / Symmetry type: POINT
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.00853042
f_angle_d1.16675528
f_dihedral_angle_d14.33923674
f_chiral_restr0.0866296
f_plane_restr0.00810126

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