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- PDB-9mgz: Dunaliella tertiolecta PSI-LHCI-TIDI1 supercomplex -

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Basic information

Entry
Database: PDB / ID: 9mgz
TitleDunaliella tertiolecta PSI-LHCI-TIDI1 supercomplex
Components
  • (Chlorophyll a-b binding protein, ...) x 3
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 4
  • LHCA3
  • PSAF1
  • PSAL1
  • PSI-K
  • Photosystem I iron-sulfur center
  • TIDI1
KeywordsPHOTOSYNTHESIS / iron homeostasis / membrane protein / photosystem I / Dunaliella / green alga / PSI-LHCI supercomplex / TIDI / thylakoid iron-deficiency induced protein / photosynthetic apparatus / eukaryotes / Dunaliella tertiolecta
Function / homology
Function and homology information


BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LMK / Chem-LUT / PHYLLOQUINONE ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LMK / Chem-LUT / PHYLLOQUINONE / PHOSPHATIDYLETHANOLAMINE / IRON/SULFUR CLUSTER / Chem-SQD / Chem-XAT
Similarity search - Component
Biological speciesDunaliella tertiolecta (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLiu, H.W. / Khera, R. / Iwai, M. / Merchant, S.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020627 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: A distinct LHCI arrangement is recruited to photosystem I in Fe-starved green algae.
Authors: Helen W Liu / Radhika Khera / Patricia Grob / Sean D Gallaher / Samuel O Purvine / Carrie D Nicora / Mary S Lipton / Krishna K Niyogi / Eva Nogales / Masakazu Iwai / Sabeeha S Merchant /
Abstract: Iron (Fe) availability limits photosynthesis at a global scale where Fe-rich photosystem (PS) I abundance is drastically reduced in Fe-poor environments. We used single-particle cryoelectron ...Iron (Fe) availability limits photosynthesis at a global scale where Fe-rich photosystem (PS) I abundance is drastically reduced in Fe-poor environments. We used single-particle cryoelectron microscopy to reveal a unique Fe starvation-dependent arrangement of light-harvesting chlorophyll (LHC) proteins where Fe starvation-induced TIDI1 is found in an additional tetramer of LHC proteins associated with PSI in and . These cosmopolitan green algae are resilient to poor Fe nutrition. TIDI1 is a distinct LHC protein that co-occurs in diverse algae with flavodoxin (an Fe-independent replacement for the Fe-containing ferredoxin). The antenna expansion in eukaryotic algae we describe here is reminiscent of the iron-starvation induced (encoding) antenna ring in cyanobacteria, which typically co-occurs with , encoding flavodoxin. Our work showcases the convergent strategies that evolved after the Great Oxidation Event to maintain PSI capacity.
History
DepositionDec 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 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: Chlorophyll a-b binding protein, chloroplastic
3: LHCA3
7: Chlorophyll a-b binding protein, chloroplastic
8: Chlorophyll a-b binding protein, chloroplastic
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II, chloroplastic
E: Photosystem I reaction center subunit IV
F: PSAF1
J: Photosystem I reaction center subunit IX
K: PSI-K
T: TIDI1
a: Chlorophyll a-b binding protein, chloroplastic
b: Chlorophyll a-b binding protein, chloroplastic
c: Chlorophyll a-b binding protein, chloroplastic
L: PSAL1
I: Photosystem I reaction center subunit VIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)740,886302
Polymers509,17918
Non-polymers231,706284
Water00
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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Chlorophyll a-b binding protein, ... , 3 types, 6 molecules 1a7c8b

#1: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 24763.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant)
#3: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 27611.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant)
#4: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 27475.346 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant)

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Protein , 6 types, 6 molecules 3CFKTL

#2: Protein LHCA3


Mass: 30707.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant)
#7: Protein Photosystem I iron-sulfur center


Mass: 8848.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant) / References: photosystem I
#10: Protein PSAF1


Mass: 24645.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant)
#12: Protein PSI-K


Mass: 12429.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant)
#13: Protein TIDI1


Mass: 38121.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant)
#14: Protein PSAL1


Mass: 20694.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant)

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

#5: Protein Photosystem I P700 chlorophyll a apoprotein A1


Mass: 83109.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant) / References: photosystem I
#6: Protein Photosystem I P700 chlorophyll a apoprotein A2


Mass: 81895.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant) / References: photosystem I

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Photosystem I reaction center subunit ... , 4 types, 4 molecules DEJI

#8: Protein Photosystem I reaction center subunit II, chloroplastic


Mass: 21171.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant)
#9: Protein Photosystem I reaction center subunit IV


Mass: 12209.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant)
#11: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4614.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant)
#15: Protein Photosystem I reaction center subunit VIII


Mass: 11031.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella tertiolecta (plant)

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Sugars , 2 types, 5 molecules

#23: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION
#25: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 13 types, 279 molecules

#16: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 185 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#18: 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


Mass: 568.871 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#19: 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


Mass: 600.870 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H56O4
#20: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C40H56
#21: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#22: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#24: 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
#26: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#27: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#28: 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
#29: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#30: Chemical ChemComp-LMK / trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium


Mass: 773.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H94NO7 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN
Sequence detailsSequences not on Uniprot but can be found in the genome accession number GSE222140 on NCBI Gene ...Sequences not on Uniprot but can be found in the genome accession number GSE222140 on NCBI Gene Expression Omnibus (GEO)

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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: Dunaliella salina PSI-LHCI-TIDI1 supercomplex / Type: COMPLEX / Entity ID: #1-#14 / Source: NATURAL
Source (natural)Organism: Dunaliella salina (plant)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11529

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2SerialEMimage acquisition
4RELIONCTF correction
7Coot0.9.8.7model fitting
9PHENIX1.21.1model refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1601273
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 217073 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 6SL5

6sl5


Accession code: 6SL5 / Source name: PDB / Type: experimental model

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