6JEO

Structure of PSI tetramer from Anabaena


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of a cyanobacterial photosystem I tetramer revealed by cryo-electron microscopy.

Kato, K.Nagao, R.Jiang, T.Y.Ueno, Y.Yokono, M.Chan, S.K.Watanabe, M.Ikeuchi, M.Shen, J.R.Akimoto, S.Miyazaki, N.Akita, F.

(2019) Nat Commun 10: 4929-4929

  • DOI: 10.1038/s41467-019-12942-8

  • PubMed 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 tetrameric PSI core isolated from a cyanobacterium, ...

    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.


    Organizational Affiliation

    Nippon Flour Mills Co., Ltd., Innovation Center, Kanagawa, 243-0041, Japan.,Graduate School of Science, Kobe University, Hyogo, 657-8501, Japan.,Graduate School of Science, Kobe University, Hyogo, 657-8501, Japan. akimoto@hawk.kobe-u.ac.jp.,Japan Science and Technology Agency, PRESTO, Saitama, 332-0012, Japan. fusamichi_a@okayama-u.ac.jp.,Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan. shen@cc.okayama-u.ac.jp.,Institute for Protein Research, Laboratory of Protein Synthesis and Expression, Osaka University, Osaka, 565-0871, Japan. naomiyazaki@tara.tsukuba.ac.jp.,Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan. fusamichi_a@okayama-u.ac.jp.,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan.,Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan. naomiyazaki@tara.tsukuba.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A1
aA, bA, cA, dA
752Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)Mutation(s): 0 
Gene Names: psaA
EC: 1.97.1.12
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
tetrameric photosystem I
Find proteins for P58576 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P58576
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A2 1
aB, bB, cB, dB
741Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)Mutation(s): 0 
Gene Names: psaB1
EC: 1.97.1.12
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
tetrameric photosystem I
Find proteins for P58565 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P58565
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem I iron-sulfur center
aC, bC, cC, dC
81Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)Mutation(s): 0 
Gene Names: psaC
EC: 1.97.1.12
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
tetrameric photosystem I
Find proteins for P0A410 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P0A410
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit II
aD, bD, cD, dD
139Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)Mutation(s): 0 
Gene Names: psaD
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
tetrameric photosystem I
Find proteins for P58573 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P58573
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit IV
aE, bE, cE, dE
70Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)Mutation(s): 0 
Gene Names: psaE
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
tetrameric photosystem I
Find proteins for P58575 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P58575
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit III
aF, bF, cF, dF
164Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)Mutation(s): 0 
Gene Names: psaF
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
tetrameric photosystem I
Find proteins for P58564 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P58564
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit VIII
aI, bI, cI, dI
46Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)Mutation(s): 0 
Gene Names: psaI
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
tetrameric photosystem I
Find proteins for P58560 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P58560
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit IX
aJ, bJ, cJ, dJ
49Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)Mutation(s): 0 
Gene Names: psaJ
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
tetrameric photosystem I
Find proteins for P58568 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P58568
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit PsaK 1
aK, bK, cK, dK
86Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)Mutation(s): 0 
Gene Names: psaK1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
tetrameric photosystem I
Find proteins for P58583 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P58583
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit XI
aL, bL, cL, dL
172Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)Mutation(s): 0 
Gene Names: psaL
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
tetrameric photosystem I
Find proteins for P58577 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P58577
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit XII
aM, bM, cM, dM
40Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)Mutation(s): 0 
Gene Names: psaM
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
tetrameric photosystem I
Find proteins for Q8YNB0 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  Q8YNB0
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem I 4.8 kDa protein
aX, bX, cX, dX
44Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)Mutation(s): 0 
Gene Names: psaX
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
tetrameric photosystem I
Find proteins for P58566 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  P58566
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
aA, aC, bA, bC, cA, cC, dA, dC
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PQN
Query on PQN

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Download CCD File 
aA, aB, bA, bB, cA, cB, dA, dB
PHYLLOQUINONE
VITAMIN K1; 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
CLA
Query on CLA

Download SDF File 
Download CCD File 
aA, aB, aF, aJ, aK, aL, aX, bA, bB, bF, bJ, bK, bL, bX, cA, cB, cF, cJ, cK, cL, cX, dA, dB, dF, dJ, dK, dL, dX
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
CL0
Query on CL0

Download SDF File 
Download CCD File 
aA, bA, cA, dA
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
 Ligand Interaction
LMG
Query on LMG

Download SDF File 
Download CCD File 
aB, bB, cB, dB
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
BCR
Query on BCR

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Download CCD File 
aA, aB, aF, aI, aJ, aL, aM, bA, bB, bF, bI, bJ, bK, bL, bM, cA, cB, cF, cI, cJ, cL, cM, dA, dB, dF, dI, dJ, dK, dL, dM
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LHG
Query on LHG

Download SDF File 
Download CCD File 
aA, aB, bA, bB, cA, cB, dA, dB
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-13
    Type: Initial release