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- PDB-6yac: Plant PSI-ferredoxin supercomplex -

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Basic information

Entry
Database: PDB / ID: 6yac
TitlePlant PSI-ferredoxin supercomplex
Components
  • (Chlorophyll a-b binding protein ...Light-harvesting complexes of green plants) x 2
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 3
  • Chlorophyll a-b binding protein, chloroplastic
  • Ferredoxin-1, chloroplastic
  • Lhca1
  • Photosystem I iron-sulfur center
  • PsaD
  • PsaE
  • PsaF
  • PsaG
  • PsaH
  • PsaL
KeywordsPHOTOSYNTHESIS / Membrane complex / photosystem I / ferredoxin / light harvesting / excitation transfer
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast ...photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / : / electron transfer activity / magnesium ion binding / integral component of membrane / metal ion binding
Similarity search - Function
4Fe-4S dicluster domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Ferredoxin [2Fe-2S], plant / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK ...4Fe-4S dicluster domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Ferredoxin [2Fe-2S], plant / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII / Chlorophyll A-B binding protein, plant and chromista / Photosystem I reaction centre subunit VIII / Photosystem I PsaL, reaction centre subunit XI superfamily / Chlorophyll A-B binding protein / Photosystem I, reaction centre subunit XI / Chlorophyll A-B binding protein / Photosystem I reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaD / PsaD / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaA/PsaB, conserved site / Photosystem I PsaA / Photosystem I PsaB / Photosystem I psaA and psaB proteins signature. / Photosystem I psaA/psaB protein / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaA/PsaB / Electron transport accessory-like domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Beta-grasp domain superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit VI / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein 3, chloroplastic / PSI-K / Photosystem I iron-sulfur center / Ferredoxin-1, chloroplastic / PSI subunit V / Uncharacterized protein / Photosystem I reaction center subunit IX ...Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit VI / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein 3, chloroplastic / PSI-K / Photosystem I iron-sulfur center / Ferredoxin-1, chloroplastic / PSI subunit V / Uncharacterized protein / Photosystem I reaction center subunit IX / Photosystem I P700 chlorophyll a apoprotein A2 / PSI-F / Uncharacterized protein / BETA-CAROTENE / Photosystem I P700 chlorophyll a apoprotein A1 / Chem-C7Z / Chem-XAT / IRON/SULFUR CLUSTER / PHYLLOQUINONE / Chem-LUT / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / FE2/S2 (INORGANIC) CLUSTER / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / CHLOROPHYLL A / CHLOROPHYLL A ISOMER / CHLOROPHYLL B / Chlorophyll a-b binding protein P4, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (pea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsCaspy, I. / Nelson, N. / Shkolnisky, Y. / Klaiman, D. / Sheinker, A.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
German-Israeli Foundation for Research and Development1483 Israel
CitationJournal: Nat Plants / Year: 2020
Title: The structure of a triple complex of plant photosystem I with ferredoxin and plastocyanin.
Authors: Ido Caspy / Anna Borovikova-Sheinker / Daniel Klaiman / Yoel Shkolnisky / Nathan Nelson /
Abstract: The ability of photosynthetic organisms to use sunlight as a sole source of energy is endowed by two large membrane complexes-photosystem I (PSI) and photosystem II (PSII). PSI and PSII are the ...The ability of photosynthetic organisms to use sunlight as a sole source of energy is endowed by two large membrane complexes-photosystem I (PSI) and photosystem II (PSII). PSI and PSII are the fundamental components of oxygenic photosynthesis, providing oxygen, food and an energy source for most living organisms on Earth. Currently, high-resolution crystal structures of these complexes from various organisms are available. The crystal structures of megadalton complexes have revealed excitation transfer and electron-transport pathways within the various complexes. PSI is defined as plastocyanin-ferredoxin oxidoreductase but a high-resolution structure of the entire triple supercomplex is not available. Here, using a new cryo-electron microscopy technique, we solve the structure of native plant PSI in complex with its electron donor plastocyanin and the electron acceptor ferredoxin. We reveal all of the contact sites and the modes of interaction between the interacting electron carriers and PSI.
History
DepositionMar 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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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
G: PsaG
H: PsaH
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit X psaK
L: PsaL
1: Lhca1
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein 3, chloroplastic
4: Chlorophyll a-b binding protein P4, chloroplastic
N: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)562,539260
Polymers368,19317
Non-polymers194,346243
Water1,00956
1


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

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

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


Mass: 82571.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: A0A0F6NFW5, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 82381.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: A0A0F6NGI2, photosystem I

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Protein , 10 types, 10 molecules CDEFGHL12N

#3: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8860.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: P10793, photosystem I
#4: Protein PsaD


Mass: 16041.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: E1C9K8*PLUS
#5: Protein PsaE


Mass: 7479.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: E1C9K6*PLUS
#6: Protein PsaF


Mass: 17137.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: A0A0M3KL12*PLUS
#7: Protein PsaG


Mass: 10678.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea)
#8: Protein PsaH


Mass: 9491.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: A0A0M3KL10*PLUS
#12: Protein PsaL


Mass: 16564.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: E1C9L1*PLUS
#13: Protein Lhca1


Mass: 21335.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea)
#14: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 22845.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: Q41038
#17: Protein Ferredoxin-1, chloroplastic / / Ferredoxin I


Mass: 10359.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: P09911

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Photosystem I reaction center subunit ... , 3 types, 3 molecules IJK

#9: Protein/peptide Photosystem I reaction center subunit VIII / / PSI-I


Mass: 3409.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: P17227
#10: Protein/peptide Photosystem I reaction center subunit IX / / PSI-J


Mass: 4767.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: D5MAL3
#11: Protein Photosystem I reaction center subunit X psaK /


Mass: 8135.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: E1C9L3

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Chlorophyll a-b binding protein ... , 2 types, 2 molecules 34

#15: Protein Chlorophyll a-b binding protein 3, chloroplastic / LHCII type III CAB-3


Mass: 24139.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: Q32904
#16: Protein Chlorophyll a-b binding protein P4, chloroplastic / LHCI type III CAB-P4


Mass: 21994.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (pea) / References: UniProt: Q9SQL2

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Sugars , 2 types, 14 molecules

#24: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#27: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 14 types, 285 molecules

#18: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#19: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 141 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#20: 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
#21: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


Mass: 536.873 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C40H56
#23: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#25: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C45H86O10
#26: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#28: 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.: 7 / Source method: obtained synthetically / Formula: C40H56O2
#29: Chemical
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#30: 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.: 2 / Source method: obtained synthetically / Formula: C40H56O4
#31: Chemical ChemComp-C7Z / (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O2
#32: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#33: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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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: Pea Photosystem I in complex with Ferredoxin / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL
Molecular weightValue: 0.66 MDa / Experimental value: NO
Source (natural)Organism: Pisum sativum (pea)
Buffer solutionpH: 8
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 / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 1.075 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3669

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18rc4_3812refinement
PHENIX1.18rc4_3812refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7PHENIXmodel fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1776870
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 269657 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-ID
15L8R1
21A701
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 48.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00840543
ELECTRON MICROSCOPYf_angle_d1.911157176
ELECTRON MICROSCOPYf_chiral_restr0.15615102
ELECTRON MICROSCOPYf_plane_restr0.01077328
ELECTRON MICROSCOPYf_dihedral_angle_d26.650916639

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