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- PDB-6yxr: Dunaliella Minimal Photosystem I -

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Basic information

Entry
Database: PDB / ID: 6yxr
TitleDunaliella Minimal Photosystem I
Components
  • (Chlorophyll a-b binding protein, ...Light-harvesting complexes of green plants) x 2
  • (Photosystem I ...) x 4
  • Lhca2
  • Lhca4
  • PsaD
  • PsaE
  • PsaF
KeywordsPHOTOSYNTHESIS / membrane complex / photosystem I / dunaliella / light harvesting / excitation transfer
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / protein-chromophore linkage ...photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / protein-chromophore linkage / electron transfer activity / magnesium ion binding / integral component of membrane / metal ion binding
Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaJ, reaction centre subunit IX superfamily / Chlorophyll a/b binding domain superfamily / Chlorophyll A-B binding protein / Photosystem I PsaA/PsaB, conserved site / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Photosystem I protein PsaC ...Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaJ, reaction centre subunit IX superfamily / Chlorophyll a/b binding domain superfamily / Chlorophyll A-B binding protein / Photosystem I PsaA/PsaB, conserved site / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / Chlorophyll A-B binding protein, plant
Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2
Biological speciesDunaliella salina (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNelson, N. / Caspy, I. / Malavath, T. / Klaiman, D. / Shkolinsky, Y.
Funding support Israel, Belgium, 2items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
European Research Council (ERC)723991 Belgium
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2020
Title: Structure and energy transfer pathways of the Dunaliella Salina photosystem I supercomplex.
Authors: Ido Caspy / Tirupathi Malavath / Daniel Klaiman / Maria Fadeeva / Yoel Shkolnisky / Nathan Nelson /
Abstract: Oxygenic photosynthesis evolved more than 3 billion years ago in cyanobacteria. The increased complexity of photosystem I (PSI) became apparent from the high-resolution structures that were obtained ...Oxygenic photosynthesis evolved more than 3 billion years ago in cyanobacteria. The increased complexity of photosystem I (PSI) became apparent from the high-resolution structures that were obtained for the complexes that were isolated from various organisms, ranging from cyanobacteria to plants. These complexes are all evolutionarily linked. In this paper, the researchers have uncovered the increased complexity of PSI in a single organism demonstrated by the coexistance of two distinct PSI compositions. The Large Dunaliella PSI contains eight additional subunits, six in PSI core and two light harvesting complexes. Two additional chlorophyll a molecules pertinent for efficient excitation energy transfer in state II transition were identified in PsaL and PsaO. Short distances between these newly identified chlorophylls correspond with fast excitation transfer rates previously reported during state II transition. The apparent PSI conformations could be a coping mechanism for the high salinity.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
1: Chlorophyll a-b binding protein, chloroplastic
2: Lhca2
3: Chlorophyll a-b binding protein, chloroplastic
4: Lhca4
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: PsaD
E: PsaE
F: PsaF
J: Photosystem I reaction center subunit IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,244205
Polymers307,63711
Non-polymers158,607194
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area278180 Å2
ΔGint-2264 kcal/mol
Surface area98210 Å2
MethodPISA

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Components

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Chlorophyll a-b binding protein, ... , 2 types, 2 molecules 13

#1: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 21305.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: C1K003
#3: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 22732.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: C1K004

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Protein , 5 types, 5 molecules 24DEF

#2: Protein Lhca2


Mass: 22813.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#4: Protein Lhca4


Mass: 23131.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#8: Protein PsaD


Mass: 15883.294 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#9: Protein PsaE


Mass: 7297.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#10: Protein PsaF


Mass: 18212.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)

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Photosystem I ... , 4 types, 4 molecules ABCJ

#5: Protein Photosystem I P700 chlorophyll a apoprotein A1 / / PSI-A / PsaA


Mass: 81748.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXV2, photosystem I
#6: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 81327.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXZ0, photosystem I
#7: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8717.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXW7, photosystem I
#11: Protein/peptide Photosystem I reaction center subunit IX / / PSI-J


Mass: 4467.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXW0

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Non-polymers , 12 types, 194 molecules

#12: 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.: 4 / Source method: obtained synthetically / Formula: C40H56O2
#13: 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.: 4 / Source method: obtained synthetically / Formula: C40H56O4
#14: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C40H56
#15: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 134 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#16: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#17: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#18: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C45H86O10
#19: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H77O8P
#20: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#21: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#22: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#23: Chemical ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15

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Details

Has ligand of interestN

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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: Large dunaliella salina photosystem I-LHC supercomplex
Type: COMPLEX / Entity ID: 1,2,3,4,5,6,7,8,9,10,11 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Dunaliella salina (plant)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 2.5 sec blotting before plunging

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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 / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 42.68 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4306

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18rc4_3812refinement
PHENIX1.18rc4_3812refinement
EM software
IDNameVersionCategory
1RELION3.0.7particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
10RELION3.0.7initial Euler assignment
11RELION3.0.7final Euler assignment
12RELION3.0.7classification
13RELION3.0.73D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 720711
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45969 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 43.33 Å2
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.021333794
ELECTRON MICROSCOPYf_angle_d2.840247988
ELECTRON MICROSCOPYf_chiral_restr0.27164080
ELECTRON MICROSCOPYf_plane_restr0.02468870
ELECTRON MICROSCOPYf_dihedral_angle_d30.378513648

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