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- PDB-9s6p: Local refinement of a PSI monomer of A. marina NIES-2412 -

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Basic information

Entry
Database: PDB / ID: 9s6p
TitleLocal refinement of a PSI monomer of A. marina NIES-2412
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 5
  • Photosystem I iron-sulfur center
  • Psa27 protein
  • PsaL
  • PsaM
  • PsaX2
KeywordsELECTRON TRANSPORT / Photosystem I / Chlorophyll d / long wavelength
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / 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 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 PsaD ...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 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 PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaA / Photosystem I protein PsaC / 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 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit PsaK ...: / CHLOROPHYLL D / CHLOROPHYLL D ISOMER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit PsaK / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Psa27 protein / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center
Similarity search - Component
Biological speciesAcaryochloris marina NIES-2412 (bacteria)
Acaryochloris marina (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.44 Å
AuthorsConsoli, G. / Leong, H.F.
Funding support Netherlands, European Union, United Kingdom, 6items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)714.018.001 Netherlands
European Research Council (ERC)European 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
CitationJournal: 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.
History
DepositionAug 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
B: Photosystem I P700 chlorophyll a apoprotein A2
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
I: Psa27 protein
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: PsaL
M: PsaM
X: PsaX2
A: Photosystem I P700 chlorophyll a apoprotein A1
C: Photosystem I iron-sulfur center
F: Photosystem I reaction center subunit III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,796137
Polymers256,41612
Non-polymers101,380125
Water70339
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 P700 chlorophyll a apoprotein ... , 2 types, 2 molecules BA

#1: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 82083.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria) / References: UniProt: A0AAT9GV97, photosystem I
#10: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PsaA


Mass: 83573.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria) / References: UniProt: A0AAT9GVI9, photosystem I

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Photosystem I reaction center subunit ... , 5 types, 5 molecules DEJKF

#2: Protein Photosystem I reaction center subunit II


Mass: 15125.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria) / References: UniProt: A0AAT9GVK4
#3: Protein Photosystem I reaction center subunit IV


Mass: 9350.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria) / References: UniProt: A0AAT9GVJ0
#5: Protein/peptide Photosystem I reaction center subunit IX


Mass: 5457.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria) / References: UniProt: B0C7S6
#6: Protein Photosystem I reaction center subunit PsaK / Photosystem I subunit X


Mass: 8894.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria) / References: UniProt: A0AAT9GVI7
#12: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 17691.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria) / References: UniProt: A0AAT9GVR1

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Protein/peptide , 3 types, 3 molecules IMX

#4: Protein/peptide Psa27 protein


Mass: 3648.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria) / References: UniProt: A0AAT9GVM8
#8: Protein/peptide PsaM


Mass: 3204.925 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina (bacteria)
#9: Protein/peptide PsaX2


Mass: 2973.575 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina (bacteria)

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Protein , 2 types, 2 molecules LC

#7: Protein PsaL


Mass: 15588.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina (bacteria)
#11: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8825.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina NIES-2412 (bacteria) / References: UniProt: B0CB42, photosystem I

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Non-polymers , 9 types, 164 molecules

#13: Chemical...
ChemComp-CL7 / CHLOROPHYLL D


Mass: 895.462 Da / Num. of mol.: 93 / Source method: obtained synthetically / Formula: C54H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O5
#15: 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
#16: 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.: 21 / Source method: obtained synthetically / Formula: C40H56
#17: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10
#18: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#19: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#20: Chemical ChemComp-G9R / CHLOROPHYLL D ISOMER


Mass: 895.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H70MgN4O6
#21: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: Photosystem I / Type: COMPLEX
Details: Chlorophyll d containing photosystem I from A. marina NIES-2412
Entity ID: #10, #1, #11, #2-#3, #12, #4-#9 / Source: NATURAL
Molecular weightValue: 0.311 MDa / Experimental value: NO
Source (natural)Organism: Acaryochloris marina (bacteria)
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
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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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: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151833 / Symmetry type: POINT
RefinementHighest resolution: 2.44 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00625247
ELECTRON MICROSCOPYf_angle_d0.72435709
ELECTRON MICROSCOPYf_dihedral_angle_d15.7624218
ELECTRON MICROSCOPYf_chiral_restr0.0513137
ELECTRON MICROSCOPYf_plane_restr0.0054609

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