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- PDB-8zeh: PSI-FCPI-L in Thalassiosira pseudonana -

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Entry
Database: PDB / ID: 8zeh
TitlePSI-FCPI-L in Thalassiosira pseudonana
Components
  • (Fucoxanthin chl a/c light-harvesting ...) x 5
  • (Fucoxanthin chlorophyll a/c light-harvesting ...) x 3
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Fucoxanthin chlorophyll a/c-binding protein Lhcq8
  • Photosystem I iron-sulfur center
  • Pt17531-like protein
  • Tp-Lhcr18
  • Tp-Lhcr20
  • Tp-PsaR
  • Tp-RedCAP
KeywordsPHOTOSYNTHESIS / photosystem I
Function / homology
Function and homology information


light-harvesting complex / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus ...light-harvesting complex / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily ...Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / 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 / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Chlorophyll A-B binding protein / Photosystem I PsaJ, reaction centre subunit IX superfamily / Chlorophyll A-B binding protein / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / : / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / 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
Chem-A86 / BETA-CAROTENE / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-ET4 / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE ...Chem-A86 / BETA-CAROTENE / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-ET4 / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit II / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Fucoxanthin chl a/c light-harvesting protein, major type / Uncharacterized protein / Fucoxanthin chlorophyll a/c light-harvesting protein / Uncharacterized protein / Fucoxanthin chl a/c light-harvesting protein / Fucoxanthin chl a/c light-harvesting protein / Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type / Fucoxanthin chl a/c light-harvesting protein / Fucoxanthin chlorophyll a/c light-harvesting protein / Uncharacterized protein / Fucoxanthin chl a/c light-harvesting protein, lhcr type / Pt17531-like protein / Photosystem I reaction center subunit IV
Similarity search - Component
Biological speciesThalassiosira pseudonana CCMP1335 (Diatom)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsFeng, Y. / Li, Z. / Wang, W. / Shen, J.R.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences2020081 China
CitationJournal: J Integr Plant Biol / Year: 2024
Title: Structures of PSI-FCPI from Thalassiosira pseudonana grown under high light provide evidence for convergent evolution and light-adaptive strategies in diatom FCPIs.
Authors: Yue Feng / Zhenhua Li / Yang Yang / Lili Shen / Xiaoyi Li / Xueyang Liu / Xiaofei Zhang / Jinyang Zhang / Fei Ren / Yuan Wang / Cheng Liu / Guangye Han / Xuchu Wang / Tingyun Kuang / Jian- ...Authors: Yue Feng / Zhenhua Li / Yang Yang / Lili Shen / Xiaoyi Li / Xueyang Liu / Xiaofei Zhang / Jinyang Zhang / Fei Ren / Yuan Wang / Cheng Liu / Guangye Han / Xuchu Wang / Tingyun Kuang / Jian-Ren Shen / Wenda Wang /
Abstract: Diatoms rely on fucoxanthin chlorophyll a/c-binding proteins (FCPs) for light harvesting and energy quenching under marine environments. Here we report two cryo-electron microscopic structures of ...Diatoms rely on fucoxanthin chlorophyll a/c-binding proteins (FCPs) for light harvesting and energy quenching under marine environments. Here we report two cryo-electron microscopic structures of photosystem I (PSI) with either 13 or five fucoxanthin chlorophyll a/c-binding protein Is (FCPIs) at 2.78 and 3.20 Å resolutions from Thalassiosira pseudonana grown under high light (HL) conditions. Among them, five FCPIs are stably associated with the PSI core, these include Lhcr3, RedCAP, Lhcq8, Lhcf10, and FCP3. The eight additional Lhcr-type FCPIs are loosely associated with the PSI core and detached under the present purification conditions. The pigments of this centric diatom showed a higher proportion of chlorophylls a, diadinoxanthins, and diatoxanthins; some of the chlorophyll as and diadinoxanthins occupy the locations of fucoxanthins found in the huge PSI-FCPI from another centric diatom Chaetoceros gracilis grown under low-light conditions. These additional chlorophyll as may form more energy transfer pathways and additional diadinoxanthins may form more energy dissipation sites relying on the diadinoxanthin-diatoxanthin cycle. These results reveal the assembly mechanism of FCPIs and corresponding light-adaptive strategies of T. pseudonana PSI-FCPI, as well as the convergent evolution of the diatom PSI-FCPI structures.
History
DepositionMay 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tp-Lhcr18
B: Fucoxanthin chlorophyll a/c-binding protein Lhcq8
C: Fucoxanthin chl a/c light-harvesting protein, major type
E: Tp-RedCAP
F: Tp-Lhcr20
G: Fucoxanthin chl a/c light-harvesting protein, lhcr type
H: Fucoxanthin chl a/c light-harvesting protein
I: Fucoxanthin chl a/c light-harvesting protein
J: Fucoxanthin chl a/c light-harvesting protein
K: Fucoxanthin chlorophyll a/c light-harvesting protein
L: Fucoxanthin chlorophyll a/c light-harvesting protein
M: Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type
a: Photosystem I P700 chlorophyll a apoprotein A1
d: Photosystem I reaction center subunit II
e: Photosystem I reaction center subunit IV
f: Photosystem I reaction center subunit III
g: Photosystem I reaction center subunit Psa29
i: Photosystem I reaction center subunit VIII
j: Photosystem I reaction center subunit IX
l: Photosystem I reaction center subunit XI
m: Photosystem I reaction center subunit XII
r: Tp-PsaR
D: Pt17531-like protein
b: Photosystem I P700 chlorophyll a apoprotein A2
c: Photosystem I iron-sulfur center
hetero molecules


Theoretical massNumber of molelcules
Total (without water)802,304391
Polymers511,13625
Non-polymers291,168366
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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Protein , 7 types, 7 molecules ABEFrDc

#1: Protein Tp-Lhcr18


Mass: 16623.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
#2: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcq8


Mass: 18249.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8C770
#4: Protein Tp-RedCAP


Mass: 20184.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
#5: Protein Tp-Lhcr20


Mass: 18561.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
#22: Protein Tp-PsaR


Mass: 9740.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8BRQ8
#23: Protein Pt17531-like protein


Mass: 18091.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8CEQ3
#25: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8675.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0W4, photosystem I

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Fucoxanthin chl a/c light-harvesting ... , 5 types, 5 molecules CGHIJ

#3: Protein Fucoxanthin chl a/c light-harvesting protein, major type


Mass: 18537.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B5YM25
#6: Protein Fucoxanthin chl a/c light-harvesting protein, lhcr type


Mass: 18926.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8C8Q0
#7: Protein Fucoxanthin chl a/c light-harvesting protein


Mass: 18522.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8C2K6
#8: Protein Fucoxanthin chl a/c light-harvesting protein


Mass: 18706.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8C0K3
#9: Protein Fucoxanthin chl a/c light-harvesting protein


Mass: 19792.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8BYV4

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Fucoxanthin chlorophyll a/c light-harvesting ... , 3 types, 3 molecules KLM

#10: Protein Fucoxanthin chlorophyll a/c light-harvesting protein


Mass: 19044.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8C2Y4
#11: Protein Fucoxanthin chlorophyll a/c light-harvesting protein


Mass: 23791.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8BU33
#12: Protein Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type


Mass: 18608.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8C0K4

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

#13: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PSI-A / PsaA


Mass: 82691.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0M8, photosystem I
#24: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82042.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0M9, photosystem I

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Photosystem I reaction center subunit ... , 8 types, 8 molecules defgijlm

#14: Protein Photosystem I reaction center subunit II


Mass: 14732.663 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0T5
#15: Protein Photosystem I reaction center subunit IV


Mass: 7133.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8LEQ8
#16: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 17617.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0V0
#17: Protein Photosystem I reaction center subunit Psa29


Mass: 13936.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8BUW3
#18: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 3604.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0S9
#19: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4707.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0V1
#20: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 15469.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0U5
#21: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3143.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0S1

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Sugars , 1 types, 1 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 11 types, 365 molecules

#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.: 27 / Source method: obtained synthetically / Formula: C40H54O3 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 229 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical
ChemComp-KC1 / Chlorophyll c1


Mass: 610.941 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C35H30MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical...
ChemComp-A86 / (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate / Fucoxanthin


Mass: 658.906 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C42H58O6 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#32: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#33: 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
#34: 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
#35: Chemical ChemComp-ET4 / (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol / Diatoxanthin


Mass: 566.856 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54O2 / Feature type: SUBJECT OF INVESTIGATION
#36: 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: Tp-PSI-FCPI-L / Type: COMPLEX
Entity ID: #2-#3, #23, #4, #7, #13, #24-#25, #14-#16, #18-#22, #5-#6, #8-#12, #1, #17
Source: NATURAL
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Buffer solutionpH: 6.5
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129097 / Symmetry type: POINT

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