6JEO

Structure of PSI tetramer from Anabaena


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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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: https://doi.org/10.1038/s41467-019-12942-8
  • Primary Citation of Related Structures:  
    6JEO

  • 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, 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

    Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth aA],
KA [auth dA],
M [auth bA],
Y [auth cA]
752Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P58576 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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UniProt GroupP58576
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2 1B [auth aB],
LA [auth dB],
N [auth bB],
Z [auth cB]
741Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P58565 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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UniProt GroupP58565
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerAA [auth cC],
C [auth aC],
MA [auth dC],
O [auth bC]
81Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A410 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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UniProt GroupP0A410
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIBA [auth cD],
D [auth aD],
NA [auth dD],
P [auth bD]
139Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58573 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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UniProt GroupP58573
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVCA [auth cE],
E [auth aE],
OA [auth dE],
Q [auth bE]
70Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58575 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIDA [auth cF],
F [auth aF],
PA [auth dF],
R [auth bF]
164Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58564 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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UniProt GroupP58564
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIEA [auth cI],
G [auth aI],
QA [auth dI],
S [auth bI]
46Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58560 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXFA [auth cJ],
H [auth aJ],
RA [auth dJ],
T [auth bJ]
49Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58568 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 1GA [auth cK],
I [auth aK],
SA [auth dK],
U [auth bK]
86Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58583 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIHA [auth cL],
J [auth aL],
TA [auth dL],
V [auth bL]
172Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58577 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIIA [auth cM],
K [auth aM],
UA [auth dM],
W [auth bM]
40Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8YNB0 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I 4.8 kDa proteinJA [auth cX],
L [auth aX],
VA [auth dX],
X [auth bX]
44Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58566 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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AB [auth aA]
AC [auth aA]
AD [auth aB]
AE [auth aB]
AF [auth aF]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

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JP [auth dA],
OK [auth cA],
RF [auth bA],
WA [auth aA]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG

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FT [auth dB],
LO [auth cB],
NJ [auth bB],
TE [auth aB]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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GR [auth dA]
GT [auth dB]
HR [auth dA]
MO [auth cB]
NM [auth cA]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR

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AK [auth bJ]
AT [auth dB]
BF [auth aF]
BP [auth cL]
BR [auth dA]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

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EO [auth cB]
FM [auth cA]
GJ [auth bB]
HH [auth bA]
ME [auth aB]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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AR [auth dA]
GM [auth cA]
IH [auth bA]
IT [auth dC]
JT [auth dC]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX1.13_2998

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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