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- PDB-6jeo: Structure of PSI tetramer from Anabaena -

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Basic information

Entry
Database: PDB / ID: 6jeo
TitleStructure of PSI tetramer from Anabaena
Components(Photosystem I ...) x 12
KeywordsPHOTOSYNTHESIS / Photosystem
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / 4Fe-4S dicluster domain / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / 4Fe-4S dicluster domain / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / 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 / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / 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 / 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
BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit III ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A2 1 / Photosystem I 4.8 kDa protein / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKato, K. / Nagao, R. / Shen, J.R. / Miyazaki, N. / Akita, F.
CitationJournal: Nat Commun / Year: 2019
Title: Structure of a cyanobacterial photosystem I tetramer revealed by cryo-electron microscopy.
Authors: Koji Kato / Ryo Nagao / Tian-Yi Jiang / Yoshifumi Ueno / Makio Yokono / Siu Kit Chan / Mai Watanabe / Masahiko Ikeuchi / Jian-Ren Shen / Seiji Akimoto / Naoyuki Miyazaki / Fusamichi Akita /
Abstract: Photosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a ...Photosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a tetrameric PSI core isolated from a cyanobacterium, Anabaena sp. PCC 7120, analysed by single-particle cryo-electron microscopy (cryo-EM) at 3.3 Å resolution. The PSI tetramer has a C2 symmetry and is organised in a dimer of dimers form. The structure reveals interactions at the dimer-dimer interface and the existence of characteristic pigment orientations and inter-pigment distances within the dimer units that are important for unique excitation energy transfer. In particular, characteristic residues of PsaL are identified to be responsible for the formation of the tetramer. Time-resolved fluorescence analyses showed that the PSI tetramer has an enhanced excitation-energy quenching. These structural and spectroscopic findings provide insights into the physiological significance of the PSI tetramer and evolutionary changes of the PSI organisations.
History
DepositionFeb 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
aA: Photosystem I P700 chlorophyll a apoprotein A1
aB: Photosystem I P700 chlorophyll a apoprotein A2 1
aC: Photosystem I iron-sulfur center
aD: Photosystem I reaction center subunit II
aE: Photosystem I reaction center subunit IV
aF: Photosystem I reaction center subunit III
aI: Photosystem I reaction center subunit VIII
aJ: Photosystem I reaction center subunit IX
aK: Photosystem I reaction center subunit PsaK 1
aL: Photosystem I reaction center subunit XI
aM: Photosystem I reaction center subunit XII
aX: Photosystem I 4.8 kDa protein
bA: Photosystem I P700 chlorophyll a apoprotein A1
bB: Photosystem I P700 chlorophyll a apoprotein A2 1
bC: Photosystem I iron-sulfur center
bD: Photosystem I reaction center subunit II
bE: Photosystem I reaction center subunit IV
bF: Photosystem I reaction center subunit III
bI: Photosystem I reaction center subunit VIII
bJ: Photosystem I reaction center subunit IX
bK: Photosystem I reaction center subunit PsaK 1
bL: Photosystem I reaction center subunit XI
bM: Photosystem I reaction center subunit XII
bX: Photosystem I 4.8 kDa protein
cA: Photosystem I P700 chlorophyll a apoprotein A1
cB: Photosystem I P700 chlorophyll a apoprotein A2 1
cC: Photosystem I iron-sulfur center
cD: Photosystem I reaction center subunit II
cE: Photosystem I reaction center subunit IV
cF: Photosystem I reaction center subunit III
cI: Photosystem I reaction center subunit VIII
cJ: Photosystem I reaction center subunit IX
cK: Photosystem I reaction center subunit PsaK 1
cL: Photosystem I reaction center subunit XI
cM: Photosystem I reaction center subunit XII
cX: Photosystem I 4.8 kDa protein
dA: Photosystem I P700 chlorophyll a apoprotein A1
dB: Photosystem I P700 chlorophyll a apoprotein A2 1
dC: Photosystem I iron-sulfur center
dD: Photosystem I reaction center subunit II
dE: Photosystem I reaction center subunit IV
dF: Photosystem I reaction center subunit III
dI: Photosystem I reaction center subunit VIII
dJ: Photosystem I reaction center subunit IX
dK: Photosystem I reaction center subunit PsaK 1
dL: Photosystem I reaction center subunit XI
dM: Photosystem I reaction center subunit XII
dX: Photosystem I 4.8 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,459,789552
Polymers1,053,36948
Non-polymers406,420504
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I ... , 12 types, 48 molecules aAbAcAdAaBbBcBdBaCbCcCdCaDbDcDdDaEbEcEdEaFbFcFdFaIbIcIdIaJbJ...

#1: Protein
Photosystem I P700 chlorophyll a apoprotein A1 / / PsaA


Mass: 83289.680 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58576, photosystem I
#2: Protein
Photosystem I P700 chlorophyll a apoprotein A2 1 / / PsaB 1


Mass: 83457.016 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58565, photosystem I
#3: Protein
Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8825.206 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P0A410, photosystem I
#4: Protein
Photosystem I reaction center subunit II /


Mass: 15176.240 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58573
#5: Protein
Photosystem I reaction center subunit IV /


Mass: 7897.051 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58575
#6: Protein
Photosystem I reaction center subunit III / / PSI-F


Mass: 17850.568 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58564
#7: Protein/peptide
Photosystem I reaction center subunit VIII /


Mass: 5066.925 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58560
#8: Protein/peptide
Photosystem I reaction center subunit IX /


Mass: 5499.422 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58568
#9: Protein
Photosystem I reaction center subunit PsaK 1 / / Photosystem I subunit X 1


Mass: 8852.457 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58583
#10: Protein
Photosystem I reaction center subunit XI / / PSI subunit V / PSI-L


Mass: 18130.725 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58577
#11: Protein/peptide
Photosystem I reaction center subunit XII / / PSI-M


Mass: 4424.250 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: Q8YNB0
#12: Protein/peptide
Photosystem I 4.8 kDa protein /


Mass: 4872.792 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / References: UniProt: P58566

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Non-polymers , 7 types, 504 molecules

#13: Chemical
ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 376 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#15: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C31H46O2
#16: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4
#17: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 88 / Source method: obtained synthetically / Formula: C40H56
#18: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#19: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10

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Details

Has ligand of interestN
Sequence detailsThe sequence was based on sequence reference BAB76356.1. The associated accession in UNIPROT, ...The sequence was based on sequence reference BAB76356.1. The associated accession in UNIPROT, Q8YNB0 (PSAM_NOSS1), differs from NCBI with translation N-terminally shortened.

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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: PSI tetramer / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Molecular weightValue: 1.44 MDa / Experimental value: NO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Buffer solutionpH: 6.5
Buffer component
IDConc.FormulaBuffer-ID
120 mMMES-NaOH1
20.04 %DDM1
SpecimenConc.: 0.014 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: (1.14_3260: phenix.real_space_refine) / Classification: refinement
EM software
IDNameVersionCategory
4Gctf1.06CTF correction
7UCSF Chimera1.12model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.13_2998model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111400 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 1JB0

1jb0

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