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- PDB-6sl5: Dunaliella Photosystem I Supercomplex -

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Basic information

Entry
Database: PDB / ID: 6sl5
TitleDunaliella Photosystem I Supercomplex
Components
  • (Chlorophyll a-b binding protein, ...Light-harvesting complexes of green plants) x 2
  • (Photosystem I ...) x 4
  • Lhca2
  • Lhca4
  • Lhca5
  • Lhca6
  • PsaD
  • PsaE
  • PsaF
  • PsaG
  • PsaH
  • PsaI
  • PsaK
  • PsaL
  • PsaO
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 / electron transfer activity ...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 / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Single helix bin / SH3 type barrels. - #50 / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ ...Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Single helix bin / SH3 type barrels. - #50 / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Alpha-Beta Plaits - #20 / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Helicase, Ruva Protein; domain 3 / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Tripalmitoylglycerol / BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LMK ...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Tripalmitoylglycerol / BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LMK / Chem-LUT / octadecanal / Chem-P3H / PHYLLOQUINONE / PHOSPHATIDYLETHANOLAMINE / IRON/SULFUR CLUSTER / Chem-SQD / Chem-XAT / 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
Similarity search - Component
Biological speciesDunaliella salina (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 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.
History
DepositionAug 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 15, 2020Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

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Assembly

Deposited unit
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
G: PsaG
H: PsaH
I: PsaI
K: PsaK
L: PsaL
O: PsaO
1: Chlorophyll a-b binding protein, chloroplastic
2: Lhca2
3: Chlorophyll a-b binding protein, chloroplastic
4: Lhca4
5: Lhca5
6: Lhca6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)644,178311
Polymers410,77419
Non-polymers233,404292
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

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


Mass: 81877.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXV2, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 81671.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXZ0, photosystem I
#3: 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
#7: Protein/peptide Photosystem I reaction center subunit IX / / PSI-J


Mass: 4614.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXW0

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Protein , 12 types, 12 molecules DEFGHKLO2456

#4: Protein PsaD


Mass: 16214.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#5: Protein PsaE


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


Mass: 18115.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#8: Protein PsaG


Mass: 10928.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#9: Protein PsaH


Mass: 10012.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#11: Protein PsaK


Mass: 8191.218 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#12: Protein PsaL


Mass: 16189.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#13: Protein PsaO


Mass: 9635.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#15: Protein Lhca2


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


Mass: 23131.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#18: Protein Lhca5


Mass: 21676.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#19: Protein Lhca6


Mass: 19559.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)

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Protein/peptide , 1 types, 1 molecules I

#10: Protein/peptide PsaI


Mass: 4236.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)

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

#14: 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
#16: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 24585.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: C1K004*PLUS

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Sugars , 2 types, 8 molecules

#27: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#28: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 18 types, 284 molecules

#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-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 172 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#22: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


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


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#24: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C40H56
#25: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#26: Chemical ChemComp-OCD / octadecanal / Octadecanal


Mass: 268.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O
#29: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID / Phosphatidic acid


Mass: 704.998 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H77O8P
#30: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#31: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C45H86O10
#32: Chemical ChemComp-4RF / Tripalmitoylglycerol / propane-1,2,3-triyl trihexadecanoate / Tripalmitin


Mass: 807.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H98O6
#33: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#34: 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 / Lutein


Mass: 568.871 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C40H56O2
#35: 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 / Violaxanthin


Mass: 600.870 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H56O4
#36: Chemical
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#37: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C41H78O12S
#38: Chemical ChemComp-LMK / trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium


Mass: 773.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C46H94NO7
#39: Chemical ChemComp-P3H / [(2~{R})-1-nonanoyloxy-3-[oxidanyl-[(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z})-heptadeca-5,8-dienoate


Mass: 722.841 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H63O13P

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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-#19 / 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
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
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
1RELION3particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7PHENIX1.18model fitting
9PHENIX1.18model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 720711
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189006 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 83 / Protocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 1.34 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011546189
ELECTRON MICROSCOPYf_angle_d2.261865216
ELECTRON MICROSCOPYf_chiral_restr0.16815653
ELECTRON MICROSCOPYf_plane_restr0.010511924
ELECTRON MICROSCOPYf_dihedral_angle_d26.487819083

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