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- PDB-9m4f: Photosystem I from the eukaryotic filamentous algae -

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Basic information

Entry
Database: PDB / ID: 9m4f
TitlePhotosystem I from the eukaryotic filamentous algae
Components
  • (light-harvesting protein ...) x 11
  • PsaA
  • PsaB
  • PsaC
  • PsaD
  • PsaE
  • PsaF
  • PsaI
  • PsaJ
  • PsaL
  • PsaM
  • PsaR
  • PsaS
KeywordsPHOTOSYNTHESIS / Photosystem I / Xanthophyceae / Tribonema minus
Function / homology: / BETA-CAROTENE / CHLOROPHYLL A / Chem-DD6 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER
Function and homology information
Biological speciesTribonema minus (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsShao, R.Q. / Pan, X.W.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2804400 China
National Natural Science Foundation of China (NSFC)32371269 China
National Natural Science Foundation of China (NSFC)32470247 China
Chinese Academy of Sciences2024kf05 China
CitationJournal: J Integr Plant Biol / Year: 2025
Title: Architecture of photosystem I-light-harvesting complex from the eukaryotic filamentous yellow-green alga Tribonema minus.
Authors: Ruiqi Shao / Yuqi Zou / Hui Shang / Yue Qiu / Zuxing Liang / Xiaodong Su / Shumeng Zhang / Mei Li / Xiaowei Pan /
Abstract: Eukaryotic photosystem I (PSI) is a multi-subunit pigment-protein supercomplex that consists of a core complex and multiple peripheral light-harvesting complexes I (LHCIs), which increases the light ...Eukaryotic photosystem I (PSI) is a multi-subunit pigment-protein supercomplex that consists of a core complex and multiple peripheral light-harvesting complexes I (LHCIs), which increases the light absorption capacity of the core complex. Throughout the evolution of oxygenic photoautotrophs, the core subunits of PSI have remained highly conserved, while LHCIs exhibit significant variability, presumably to adapt to diverse environments. This study presents a 2.82 Å resolution structure of PSI from the filamentous yellow-green alga Tribonema minus (Tm), a member of the class Xanthophyceae that evolved from red algae through endosymbiosis and is considered a promising candidate for biofuel production due to its high biomass and lipid content. Our structure reveals a supramolecular organization consisting of 12 core subunits and 13 LHCIs, here referred to as Xanthophyceae light-harvesting complexes (XLHs), along with the arrangement of pigments within the TmPSI-XLH supercomplex. A structural comparison between TmPSI-XLH and PSI-LHCI from various red lineages highlights distinctive features of TmPSI-XLH, suggesting that it represents a unique intermediate state in the PSI assembly process during the evolutionary transition from red algae to diatoms. Our findings advance the understanding of the molecular mechanisms responsible for energy transfer in Xanthophyceae PSI-XLH and the evolutionary adaptation of red lineages.
History
DepositionMar 4, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Light-harvesting protein XLH1
2: light-harvesting protein XLH2
3: light-harvesting protein XLH3
4: light-harvesting protein XLH4
5: light-harvesting protein XLH5
6: light-harvesting protein XLH6/10
7: light-harvesting protein XLH7
8: light-harvesting protein XLH8
9: light-harvesting protein XLH9/13
h: light-harvesting protein XLH6/10
c: light-harvesting protein XLH11
t: light-harvesting protein XLH12
k: light-harvesting protein XLH9/13
A: PsaA
B: PsaB
C: PsaC
D: PsaD
E: PsaE
F: PsaF
I: PsaI
J: PsaJ
L: PsaL
M: PsaM
R: PsaR
S: PsaS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)825,594363
Polymers557,19525
Non-polymers268,398338
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Light-harvesting protein ... , 11 types, 13 molecules 123456h789kct

#1: Protein Light-harvesting protein XLH1


Mass: 23276.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#2: Protein light-harvesting protein XLH2


Mass: 20953.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#3: Protein light-harvesting protein XLH3


Mass: 21701.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#4: Protein light-harvesting protein XLH4


Mass: 24273.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#5: Protein light-harvesting protein XLH5


Mass: 22618.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#6: Protein light-harvesting protein XLH6/10


Mass: 22235.654 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#7: Protein light-harvesting protein XLH7


Mass: 22124.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#8: Protein light-harvesting protein XLH8


Mass: 19510.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#9: Protein light-harvesting protein XLH9/13


Mass: 23143.885 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#10: Protein light-harvesting protein XLH11


Mass: 21832.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#11: Protein light-harvesting protein XLH12


Mass: 24538.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)

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Protein , 9 types, 9 molecules ABCDEFLRS

#12: Protein PsaA


Mass: 83163.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#13: Protein PsaB


Mass: 82145.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#14: Protein PsaC


Mass: 8737.103 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#15: Protein PsaD


Mass: 15405.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#16: Protein PsaE


Mass: 7013.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#17: Protein PsaF


Mass: 20668.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#20: Protein PsaL


Mass: 15801.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#22: Protein PsaR


Mass: 9267.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#23: Protein PsaS


Mass: 11422.071 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)

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Protein/peptide , 3 types, 3 molecules IJM

#18: Protein/peptide PsaI


Mass: 3940.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#19: Protein/peptide PsaJ


Mass: 4792.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)
#21: Protein/peptide PsaM


Mass: 3249.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tribonema minus (eukaryote)

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Sugars , 1 types, 7 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 8 types, 331 molecules

#24: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 230 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical...
ChemComp-DD6 / (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol / Diadinoxanthin


Mass: 582.855 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: C40H54O3 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#29: Chemical
ChemComp-A1L1G / (1~{R},3~{S})-6-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{Z},17~{E})-16-(hydroxymethyl)-3,7,12-trimethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]-1,5,5-trimethyl-cyclohexane-1,3-diol


Mass: 616.870 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H56O5 / Feature type: SUBJECT OF INVESTIGATION
#30: 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
#31: 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 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION

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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-Light-Harvesting Complexes from the Eukaryotic Filamentous Yellow-Green Algae Tribonema minus
Type: COMPLEX / Entity ID: #1-#23 / Source: NATURAL
Source (natural)Organism: Tribonema minus (eukaryote)
Buffer solutionpH: 7.5
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: Tecnai Spirit / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI SPIRIT
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60389 / Symmetry type: POINT
RefinementHighest resolution: 2.82 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.05102433
ELECTRON MICROSCOPYf_angle_d1.22186287
ELECTRON MICROSCOPYf_dihedral_angle_d19.36926555
ELECTRON MICROSCOPYf_chiral_restr0.0476567
ELECTRON MICROSCOPYf_plane_restr0.01314969

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