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- PDB-8wgh: Cryo-EM structure of the red-shifted Fittonia albivenis PSI-LHCI -

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Basic information

Entry
Database: PDB / ID: 8wgh
TitleCryo-EM structure of the red-shifted Fittonia albivenis PSI-LHCI
Components
  • (Chlorophyll a-b binding protein ...) x 4
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 11
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Complex
Function / homology
Function and homology information


chloroplast thylakoid / plastoglobule / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope / photosystem I / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane ...chloroplast thylakoid / plastoglobule / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope / photosystem I / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / protein domain specific binding / mRNA binding / magnesium ion binding / nucleus / metal ion binding
Similarity search - Function
4Fe-4S dicluster domain / 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 / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ ...4Fe-4S dicluster domain / 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 / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I protein PsaC / Photosystem I PsaA / 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 / 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
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit VIII / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III, chloroplastic
Similarity search - Component
Biological speciesFittonia albivenis (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsHuang, G.Q. / Li, X.X. / Sui, S.F. / Qin, X.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the red-shifted Fittonia albivenis PSI-LHCI
Authors: Huang, G.Q. / Li, X.X. / Sui, S.F. / Qin, X.C.
History
DepositionSep 21, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: 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 1
2: Chlorophyll a-b binding protein 2
3: Chlorophyll a-b binding protein 3
4: Chlorophyll a-b binding protein 4
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
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III, chloroplastic
G: Photosystem I reaction center subunit VIII
H: Photosystem I reaction center subunit VI
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit psaK
L: Photosystem I reaction center subunit XI
N: Photosystem I reaction center subunit N
O: Photosystem I reaction center subunit O
hetero molecules


Theoretical massNumber of molelcules
Total (without water)637,515243
Polymers459,41118
Non-polymers178,105225
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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Chlorophyll a-b binding protein ... , 4 types, 4 molecules 1234

#1: Protein Chlorophyll a-b binding protein 1


Mass: 26773.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant)
#2: Protein Chlorophyll a-b binding protein 2


Mass: 28533.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant)
#3: Protein Chlorophyll a-b binding protein 3


Mass: 29766.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant)
#4: Protein Chlorophyll a-b binding protein 4


Mass: 27510.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (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 / PSI-A / PsaA


Mass: 83138.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A8A0WPY6.
Source: (natural) Fittonia albivenis (plant) / References: UniProt: A0A8A0WPY6, photosystem I
#6: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82472.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id G9IB61.
Source: (natural) Fittonia albivenis (plant) / References: UniProt: G9IB61, photosystem I

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Protein , 1 types, 1 molecules C

#7: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 9049.509 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A4QJG7.
Source: (natural) Fittonia albivenis (plant) / References: UniProt: A4QJG7, photosystem I

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Photosystem I reaction center subunit ... , 11 types, 11 molecules DEFGHIJKLNO

#8: Protein Photosystem I reaction center subunit II


Mass: 21036.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant)
#9: Protein Photosystem I reaction center subunit IV


Mass: 16282.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant)
#10: Protein Photosystem I reaction center subunit III, chloroplastic / Light-harvesting complex I 17 kDa protein / PSI-F


Mass: 24203.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id Q9SHE8.
Source: (natural) Fittonia albivenis (plant) / References: UniProt: Q9SHE8
#11: Protein Photosystem I reaction center subunit VIII


Mass: 15873.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant)
#12: Protein Photosystem I reaction center subunit VI


Mass: 15201.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant)
#13: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 3930.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A8A9WIB9.
Source: (natural) Fittonia albivenis (plant) / References: UniProt: A0A8A9WIB9
#14: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 5029.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id Q3C1K9.
Source: (natural) Fittonia albivenis (plant) / References: UniProt: Q3C1K9
#15: Protein Photosystem I reaction center subunit psaK


Mass: 13435.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant)
#16: Protein Photosystem I reaction center subunit XI


Mass: 23094.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant)
#17: Protein Photosystem I reaction center subunit N


Mass: 18673.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant)
#18: Protein Photosystem I reaction center subunit O


Mass: 15404.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fittonia albivenis (plant)

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Sugars , 3 types, 13 molecules

#26: Sugar
ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#29: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#30: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 9 types, 212 molecules

#19: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 150 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#21: 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.: 7 / Source method: obtained synthetically / Formula: C40H56O2
#22: 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.: 4 / Source method: obtained synthetically / Formula: C40H56O4
#23: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C40H56
#24: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#25: 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
#27: 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
#28: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4

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Details

Has ligand of interestY

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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 complex / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL
Source (natural)Organism: Fittonia albivenis (plant)
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: 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: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157342 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00440422
ELECTRON MICROSCOPYf_angle_d1.42157465
ELECTRON MICROSCOPYf_dihedral_angle_d21.1026820
ELECTRON MICROSCOPYf_chiral_restr0.0664940
ELECTRON MICROSCOPYf_plane_restr0.0057598

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