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Basic information

Entry
Database: PDB / ID: 7coy
TitleStructure of the far-red light utilizing photosystem I of Acaryochloris marina
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I protein ...) x 5
  • (Photosystem I reaction center subunit ...) x 3
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Photosystem I / Acaryochloris marina / Light-harvesting / Chlorophyll d
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I PsaF, reaction centre subunit III ...Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / 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 / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 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
CHLOROPHYLL D / CHLOROPHYLL D ISOMER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 ...CHLOROPHYLL D / CHLOROPHYLL D ISOMER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Photosystem I reaction center subunit II / Photosystem I reaction center subunit PsaK / Photosystem I iron-sulfur center
Similarity search - Component
Biological speciesAcaryochloris marina MBIC11017 (bacteria)
Acaryochloris marina MBIC110017 (bacteria)
Acaryochloris marina MBIC 11017 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsKawakami, K. / Yonekura, K. / Hamaguchi, T. / Kashino, Y. / Shinzawa-Itoh, K. / Inoue-Kashino, N. / Itoh, S. / Ifuku, K. / Yamashita, E.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H05175 Japan
Japan Society for the Promotion of Science (JSPS)16H04757 Japan
Japan Society for the Promotion of Science (JSPS)16H06554 Japan
Japan Society for the Promotion of Science (JSPS)20K06684 Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Nat Commun / Year: 2021
Title: Structure of the far-red light utilizing photosystem I of Acaryochloris marina.
Authors: Tasuku Hamaguchi / Keisuke Kawakami / Kyoko Shinzawa-Itoh / Natsuko Inoue-Kashino / Shigeru Itoh / Kentaro Ifuku / Eiki Yamashita / Kou Maeda / Koji Yonekura / Yasuhiro Kashino /
Abstract: Acaryochloris marina is one of the cyanobacterial species that can use far-red light to drive photochemical reactions for oxygenic photosynthesis. Here, we report the structure of A. marina ...Acaryochloris marina is one of the cyanobacterial species that can use far-red light to drive photochemical reactions for oxygenic photosynthesis. Here, we report the structure of A. marina photosystem I (PSI) reaction center, determined by cryo-electron microscopy at 2.58 Å resolution. The structure reveals an arrangement of electron carriers and light-harvesting pigments distinct from other type I reaction centers. The paired chlorophyll, or special pair (also referred to as P740 in this case), is a dimer of chlorophyll d and its epimer chlorophyll d'. The primary electron acceptor is pheophytin a, a metal-less chlorin. We show the architecture of this PSI reaction center is composed of 11 subunits and we identify key components that help explain how the low energy yield from far-red light is efficiently utilized for driving oxygenic photosynthesis.
History
DepositionAug 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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Assembly

Deposited unit
aA: Photosystem I P700 chlorophyll a apoprotein A1
aB: Photosystem I P700 chlorophyll a apoprotein A2
aC: Photosystem I iron-sulfur center
aD: Photosystem I protein PsaD
aE: Photosystem I reaction center subunit IV
aF: Photosystem I protein PsaF
aI: Photosystem I protein Psa27
aJ: Photosystem I reaction center subunit IX
aK: Photosystem I reaction center subunit PsaK
aL: Photosystem I protein PsaL
aM: Photosystem I protein PsaM
bA: Photosystem I P700 chlorophyll a apoprotein A1
bB: Photosystem I P700 chlorophyll a apoprotein A2
bC: Photosystem I iron-sulfur center
bD: Photosystem I protein PsaD
bE: Photosystem I reaction center subunit IV
bF: Photosystem I protein PsaF
bI: Photosystem I protein Psa27
bJ: Photosystem I reaction center subunit IX
bK: Photosystem I reaction center subunit PsaK
bL: Photosystem I protein PsaL
bM: Photosystem I protein PsaM
cA: Photosystem I P700 chlorophyll a apoprotein A1
cB: Photosystem I P700 chlorophyll a apoprotein A2
cC: Photosystem I iron-sulfur center
cD: Photosystem I protein PsaD
cE: Photosystem I reaction center subunit IV
cF: Photosystem I protein PsaF
cI: Photosystem I protein Psa27
cJ: Photosystem I reaction center subunit IX
cK: Photosystem I reaction center subunit PsaK
cL: Photosystem I protein PsaL
cM: Photosystem I protein PsaM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)971,743312
Polymers763,21433
Non-polymers208,529279
Water1,51384
1


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

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 6 molecules aAbAcAaBbBcB

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


Mass: 83470.539 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 / References: UniProt: B0C474, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PsaB


Mass: 82210.555 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Acaryochloris marina MBIC110017 (bacteria)
Strain: MBIC 11017 / References: UniProt: B0C475, photosystem I

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Protein , 1 types, 3 molecules aCbCcC

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


Mass: 8825.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Acaryochloris marina MBIC110017 (bacteria)
Strain: MBIC 11017 / References: UniProt: B0CB42, photosystem I

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Photosystem I protein ... , 5 types, 15 molecules aDbDcDaFbFcFaIbIcIaLbLcLaMbMcM

#4: Protein Photosystem I protein PsaD /


Mass: 15114.146 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Acaryochloris marina MBIC110017 (bacteria)
Strain: MBIC 11017 / References: UniProt: B0C8F1
#6: Protein Photosystem I protein PsaF /


Mass: 17844.621 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Acaryochloris marina MBIC110017 (bacteria)
Strain: MBIC 11017 / References: UniProt: B0C7S7
#7: Protein/peptide Photosystem I protein Psa27 /


Mass: 3648.337 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017
#10: Protein Photosystem I protein PsaL /


Mass: 15349.588 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Acaryochloris marina MBIC 11017 (bacteria)
Strain: MBIC 11017 / References: UniProt: B0C7S4
#11: Protein/peptide Photosystem I protein PsaM /


Mass: 3190.899 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017

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Photosystem I reaction center subunit ... , 3 types, 9 molecules aEbEcEaJbJcJaKbKcK

#5: Protein Photosystem I reaction center subunit IV /


Mass: 9560.822 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Acaryochloris marina MBIC110017 (bacteria)
Strain: MBIC 11017 / References: UniProt: B0C5D5
#8: Protein Photosystem I reaction center subunit IX /


Mass: 5900.939 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Acaryochloris marina MBIC110017 (bacteria)
Strain: MBIC 11017 / References: UniProt: B0C7S6
#9: Protein Photosystem I reaction center subunit PsaK / / Photosystem I subunit X


Mass: 9289.071 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Acaryochloris marina MBIC 11017 (bacteria)
Strain: MBIC 11017 / References: UniProt: B0CA71

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Non-polymers , 9 types, 363 molecules

#12: Chemical ChemComp-G9R / CHLOROPHYLL D ISOMER


Mass: 895.462 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C54H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C55H74N4O5 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical...
ChemComp-CL7 / CHLOROPHYLL D / Chlorophyll d


Mass: 895.462 Da / Num. of mol.: 210 / Source method: obtained synthetically / Formula: C54H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 36 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#17: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#20: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Nonpolymer detailsAuthors state that Photosystem I from Acaryochloris marina contains alfa-carotene instead of beta- ...Authors state that Photosystem I from Acaryochloris marina contains alfa-carotene instead of beta-carotene. The alfa-carotene molecule possesses two rings (known as beta- and epsilon-rings) at each end, while the beta-carotene possesses two beta-rings. From the cryo-EM density map, they could not distinguish the difference between beta- and epsilon-ring, because the only difference between beta- and epsilon-ring is the arrangement of the hydrogen atom. Therefore such unclear molecules have been assigned to UNL.

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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: Photosystem I complex from Acaryochloris marina / Type: COMPLEX / Entity ID: #1-#11 / Source: NATURAL
Source (natural)Organism: Acaryochloris marina (bacteria)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 85.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86419 / Symmetry type: POINT
RefinementHighest resolution: 2.5 Å

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