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- PDB-9sk3: Trimeric photosystem I of Acaryochloris marina NIES-2412 -

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Basic information

Entry
Database: PDB / ID: 9sk3
TitleTrimeric photosystem I of Acaryochloris marina NIES-2412
Components(Photosystem I protein ...) x 12
KeywordsELECTRON TRANSPORT / Chlorophyll d / photosystem I
Function / homology: / CHLOROPHYLL D / CHLOROPHYLL D ISOMER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / PHYLLOQUINONE / IRON/SULFUR CLUSTER
Function and homology information
Biological speciesAcaryochloris marina NIES-2412 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsLeong, H.F. / Consoli, G.
Funding support Netherlands, European Union, United Kingdom, 12items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)714.018.001 Netherlands
European Research Council (ERC)101141764European Union
UK Research and Innovation (UKRI)MR/T017546/1 United Kingdom
UK Research and Innovation (UKRI)MR/T017546/2 United Kingdom
UK Research and Innovation (UKRI)MR/Y011635/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X019284/1 United Kingdom
H2020 Marie Curie Actions of the European Commission955520European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001383/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002015/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00921X United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Z516740/1 United Kingdom
Leverhulme TrustRPG-2022-203 United Kingdom
Citation
Journal: Sci Adv / Year: 2026
Title: Far-red chlorophyll d clusters extend photosystem I absorption toward the red limit.
Authors: Thomas J Oliver / Eduard Elias / Giovanni Consoli / Ho Fong Leong / Violeta Cordón-Preciado / Andrea Fantuzzi / Tanai Cardona / A William Rutherford / Roberta Croce /
Abstract: Oxygenic photosynthesis is usually limited to visible light, but the marine cyanobacterium pushes this boundary by harvesting far-red photons with chlorophyll d. The best-studied strain, MBIC11017, ...Oxygenic photosynthesis is usually limited to visible light, but the marine cyanobacterium pushes this boundary by harvesting far-red photons with chlorophyll d. The best-studied strain, MBIC11017, unexpectedly lacks low-energy chlorophylls ("red forms") in photosystem I, limiting absorption beyond 740 nanometers. Here, we show that another strain, NIES-2412, has evolved a strategy to absorb far-red photons up to 760 nanometers. Combining time-resolved fluorescence spectroscopy with cryo-electron microscopy at 2.64-angstrom resolution, we identify two distinct classes of chlorophyll d red forms in its photosystem I. One class originates from classical charge-transfer-exciton mixing, while the other arises purely from excitonic interactions. Mapping all 96 chlorophylls d reveals the precise pigments responsible for these far-red states. We also uncover a previously unreported subunit, PsaX2, which stabilizes the photosystem I complex and shapes pigment geometry and energetics to enable the formation of red forms. Last, we show that the protein modifications responsible for binding and tuning these red forms are widespread across the genus but not within the model MBIC11017 strain. Far-red photons lie close to the energetic limit of oxygenic photosynthesis; their efficient use therefore requires fine-tuning of the photosynthetic machinery. To our knowledge, our findings provide the structural and mechanistic basis of one of the most red-shifted photosystem I complexes identified to date, highlighting a distinct adaptive strategy in far-red light environments and offering design principles for extending photosynthesis in crops into the infrared.
#1: Journal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
History
DepositionSep 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
aA: Photosystem I protein PsaA
aB: Photosystem I protein PsaB
aC: Photosystem I protein PsaC
aD: Photosystem I protein PsaD
aE: Photosystem I protein PsaE
aF: Photosystem I protein PsaF
aI: Photosystem I protein PsaI
aJ: Photosystem I protein PsaJ
aK: Photosystem I protein PsaK
aL: Photosystem I protein PsaL
aM: Photosystem I protein PsaM
aX: Photosystem I protein PsaX2
bA: Photosystem I protein PsaA
bB: Photosystem I protein PsaB
bC: Photosystem I protein PsaC
bD: Photosystem I protein PsaD
bE: Photosystem I protein PsaE
bF: Photosystem I protein PsaF
bI: Photosystem I protein PsaI
bJ: Photosystem I protein PsaJ
bK: Photosystem I protein PsaK
bL: Photosystem I protein PsaL
bM: Photosystem I protein PsaM
bX: Photosystem I protein PsaX2
cA: Photosystem I protein PsaA
cB: Photosystem I protein PsaB
cC: Photosystem I protein PsaC
cD: Photosystem I protein PsaD
cE: Photosystem I protein PsaE
cF: Photosystem I protein PsaF
cI: Photosystem I protein PsaI
cJ: Photosystem I protein PsaJ
cK: Photosystem I protein PsaK
cL: Photosystem I protein PsaL
cM: Photosystem I protein PsaM
cX: Photosystem I protein PsaX2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,070,166405
Polymers769,24836
Non-polymers300,917369
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Photosystem I protein ... , 12 types, 36 molecules aAbAcAaBbBcBaCbCcCaDbDcDaEbEcEaFbFcFaIbIcIaJbJcJaKbKcKaLbLcL...

#1: Protein Photosystem I protein PsaA


Mass: 83573.766 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria)
#2: Protein Photosystem I protein PsaB


Mass: 82083.172 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria)
#3: Protein Photosystem I protein PsaC


Mass: 8825.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria)
#4: Protein Photosystem I protein PsaD


Mass: 15125.150 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria)
#5: Protein Photosystem I protein PsaE


Mass: 9350.654 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria)
#6: Protein Photosystem I protein PsaF


Mass: 17691.422 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria)
#7: Protein/peptide Photosystem I protein PsaI


Mass: 3648.337 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria)
#8: Protein/peptide Photosystem I protein PsaJ


Mass: 5457.358 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria)
#9: Protein Photosystem I protein PsaK


Mass: 8894.473 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria)
#10: Protein Photosystem I protein PsaL


Mass: 15588.004 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria)
#11: Protein/peptide Photosystem I protein PsaM


Mass: 3204.925 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria)
#12: Protein/peptide Photosystem I protein PsaX2


Mass: 2973.575 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria)

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Non-polymers , 9 types, 462 molecules

#13: Chemical ChemComp-G9R / CHLOROPHYLL D ISOMER


Mass: 895.462 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C54H70MgN4O6
#14: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C55H74N4O5
#15: Chemical...
ChemComp-CL7 / CHLOROPHYLL D


Mass: 895.462 Da / Num. of mol.: 279 / Source method: obtained synthetically / Formula: C54H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H46O2
#17: Chemical...
ChemComp-A1JPJ / (6'S)-beta,epsilon-carotene / 1,3,3-trimethyl-2-[(1~{E},4~{E},6~{E},8~{E},10~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S})-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,4,6,8,10,13,15,17-octaenyl]cyclohexene


Mass: 536.873 Da / Num. of mol.: 57 / Source method: obtained synthetically / Formula: C40H56
#18: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


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


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10
#20: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4
#21: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: Trimeric PSI / Type: COMPLEX / Details: trimeric photosystem I from A. marina NIES - 2412 / Entity ID: #4-#5, #11-#12 / Source: NATURAL
Molecular weightValue: 0.922 MDa / Experimental value: NO
Source (natural)Organism: Acaryochloris marina (bacteria) / Strain: NIES-2412
Buffer solutionpH: 6.5
Details: 50 mM MES, 1 M betaine monohydrate, 20 mM CaCl2, 5 mM MgCl2 and 10% (v/v) glycerol, pH 6.5 adjusted with NaOH
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
Image scansWidth: 5120 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151833 / Symmetry type: POINT

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