7DR0 | pdb_00007dr0

Structure of Wild-type PSI monomer1 from Cyanophora paradoxa


Experimental Data Snapshot

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

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This is version 1.2 of the entry. See complete history


Literature

Structure of a tetrameric photosystem I from a glaucophyte alga Cyanophora paradoxa.

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

(2022) Nat Commun 13: 1679-1679

  • DOI: https://doi.org/10.1038/s41467-022-29303-7
  • Primary Citation of Related Structures:  
    7DR0, 7DR1, 7DR2

  • PubMed Abstract: 

    Photosystem I (PSI) is one of the two photosystems functioning in light-energy harvesting, transfer, and electron transfer in photosynthesis. However, the oligomerization state of PSI is variable among photosynthetic organisms. We present a 3.8-Å resolution cryo-electron microscopic structure of tetrameric PSI isolated from the glaucophyte alga Cyanophora paradoxa, which reveals differences with PSI from other organisms in subunit composition and organization. The PSI tetramer is organized in a dimer of dimers with a C2 symmetry. Unlike cyanobacterial PSI tetramers, two of the four monomers are rotated around 90°, resulting in a completely different pattern of monomer-monomer interactions. Excitation-energy transfer among chlorophylls differs significantly between Cyanophora and cyanobacterial PSI tetramers. These structural and spectroscopic features reveal characteristic interactions and excitation-energy transfer in the Cyanophora PSI tetramer, suggesting that the Cyanophora PSI could represent a turning point in the evolution of PSI from prokaryotes to eukaryotes.


  • 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 A1752Cyanophora paradoxaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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UniProt GroupP48112
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2737Cyanophora paradoxaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Cyanophora paradoxaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P31173 (Cyanophora paradoxa)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, cyanelle220Cyanophora paradoxaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9T4W8 (Cyanophora paradoxa)
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UniProt GroupQ9T4W8
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV70Cyanophora paradoxaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III186Cyanophora paradoxaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]35Cyanophora paradoxaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]40Cyanophora paradoxaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 1I [auth K]157Cyanophora paradoxaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIJ [auth L]146Cyanophora paradoxaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIK [auth M]31Cyanophora paradoxaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P48185 (Cyanophora paradoxa)
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL0
Query on CL0

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L [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA
Query on CLA

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AA [auth A]
AB [auth A]
AC [auth B]
BA [auth A]
BB [auth A]
AA [auth A],
AB [auth A],
AC [auth B],
BA [auth A],
BB [auth A],
BC [auth B],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth F],
DA [auth A],
DC [auth B],
EA [auth A],
EC [auth B],
ED [auth J],
FA [auth A],
FC [auth B],
GA [auth A],
GC [auth B],
HA [auth A],
HC [auth B],
IA [auth A],
IC [auth B],
ID [auth K],
JA [auth A],
JC [auth B],
KA [auth A],
KC [auth B],
KD [auth K],
LA [auth A],
LC [auth B],
M [auth A],
MA [auth A],
MB [auth B],
MC [auth B],
MD [auth L],
N [auth A],
NA [auth A],
NB [auth B],
NC [auth B],
ND [auth L],
O [auth A],
OA [auth A],
OB [auth B],
OC [auth B],
OD [auth L],
P [auth A],
PA [auth A],
PB [auth B],
PC [auth B],
Q [auth A],
QA [auth A],
QB [auth B],
QC [auth B],
R [auth A],
RA [auth A],
RB [auth B],
RC [auth B],
S [auth A],
SA [auth A],
SB [auth B],
SC [auth B],
T [auth A],
TA [auth A],
TB [auth B],
U [auth A],
UA [auth A],
UB [auth B],
V [auth A],
VA [auth A],
VB [auth B],
W [auth A],
WA [auth A],
WB [auth B],
X [auth A],
XA [auth A],
XB [auth B],
Y [auth A],
YA [auth A],
YB [auth B],
Z [auth A],
ZA [auth A],
ZB [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

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XC [auth B]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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KB [auth A],
LB [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR

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AD [auth F]
BD [auth F]
DD [auth I]
FB [auth A]
FD [auth J]
AD [auth F],
BD [auth F],
DD [auth I],
FB [auth A],
FD [auth J],
GB [auth A],
GD [auth J],
HB [auth A],
HD [auth J],
IB [auth A],
JB [auth A],
JD [auth K],
LD [auth L],
PD [auth L],
QD [auth L],
RD [auth M],
UC [auth B],
VC [auth B],
WC [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

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DB [auth A],
TC [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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EB [auth A],
YC [auth C],
ZC [auth C]
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
MODEL REFINEMENTPHENIX1.13_2998
RECONSTRUCTIONRELION3

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2025-11-19
    Changes: Data collection, Database references