7DR2 | pdb_00007dr2

Structure of GraFix PSI tetramer from Cyanophora paradoxa

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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 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.

Macromolecule Content 

  • Total Structure Weight: 1,399.74 kDa 
  • Atom Count: 89,952 
  • Modeled Residue Count: 8,588 
  • Deposited Residue Count: 9,506 
  • Unique protein chains: 11

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth aA],
GA [auth dA],
L [auth bA],
V [auth cA]		752Cyanophora paradoxaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A097PBL3 (Cyanophora paradoxa)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B [auth aB],
HA [auth dB],
M [auth bB],
W [auth cB]		737Cyanophora paradoxaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P48113 (Cyanophora paradoxa)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC [auth aC],
IA [auth dC],
N [auth bC],
X [auth cC]		81Cyanophora paradoxaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P31173 (Cyanophora paradoxa)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, cyanelleD [auth aD],
JA [auth dD],
O [auth bD],
Y [auth cD]		220Cyanophora paradoxaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9T4W8 (Cyanophora paradoxa)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVE [auth aE],
KA [auth dE],
P [auth bE],
Z [auth cE]		70Cyanophora paradoxaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P48114 (Cyanophora paradoxa)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIAA [auth cF],
F [auth aF],
LA [auth dF],
Q [auth bF]		186Cyanophora paradoxaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P48115 (Cyanophora paradoxa)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIBA [auth cI],
G [auth aI],
MA [auth dI],
R [auth bI]		35Cyanophora paradoxaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXCA [auth cJ],
H [auth aJ],
NA [auth dJ],
S [auth bJ]		40Cyanophora paradoxaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P48117 (Cyanophora paradoxa)
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 1DA [auth cK],
I [auth aK]		157Cyanophora paradoxaMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIEA [auth cL],
J [auth aL],
OA [auth dL],
T [auth bL]		146Cyanophora paradoxaMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIFA [auth cM],
K [auth aM],
PA [auth dM],
U [auth bM]		31Cyanophora paradoxaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P48185 (Cyanophora paradoxa)
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA


Download:Ideal Coordinates CCD File
AB [auth aA]
AC [auth aA]
AD [auth aB]
AF [auth bA]
AG [auth bA]
AB [auth aA],
AC [auth aA],
AD [auth aB],
AF [auth bA],
AG [auth bA],
AI [auth bB],
AK [auth cA],
AL [auth cB],
AM [auth cB],
AN [auth cK],
AO [auth dA],
AP [auth dA],
AQ [auth dB],
AR [auth dF],
BB [auth aA],
BC [auth aA],
BD [auth aB],
BF [auth bA],
BG [auth bA],
BH [auth bB],
BI [auth bB],
BK [auth cA],
BM [auth cB],
BN [auth cK],
BO [auth dA],
BQ [auth dB],
CB [auth aA],
CC [auth aA],
CD [auth aB],
CF [auth bA],
CG [auth bA],
CH [auth bB],
CI [auth bB],
CJ [auth cA],
CK [auth cA],
CL [auth cB],
CM [auth cB],
CO [auth dA],
CQ [auth dB],
DB [auth aA],
DC [auth aA],
DD [auth aB],
DF [auth bA],
DG [auth bA],
DH [auth bB],
DI [auth bB],
DJ [auth cA],
DK [auth cA],
DL [auth cB],
DM [auth cB],
DN [auth cL],
DO [auth dA],
DQ [auth dB],
DR [auth dJ],
EB [auth aA],
EC [auth aA],
ED [auth aB],
EE [auth aF],
EF [auth bA],
EG [auth bA],
EH [auth bB],
EI [auth bB],
EJ [auth cA],
EK [auth cA],
EL [auth cB],
EM [auth cB],
EN [auth cL],
EO [auth dA],
EQ [auth dB],
FB [auth aA],
FC [auth aA],
FD [auth aB],
FF [auth bA],
FG [auth bA],
FH [auth bB],
FI [auth bB],
FJ [auth cA],
FK [auth cA],
FL [auth cB],
FM [auth cB],
FN [auth cL],
FO [auth dA],
FQ [auth dB],
GB [auth aA],
GC [auth aA],
GD [auth aB],
GF [auth bA],
GG [auth bA],
GH [auth bB],
GJ [auth cA],
GK [auth cA],
GL [auth cB],
GM [auth cB],
GO [auth dA],
GQ [auth dB],
HB [auth aA],
HD [auth aB],
HE [auth aF],
HF [auth bA],
HG [auth bA],
HH [auth bB],
HJ [auth cA],
HK [auth cA],
HL [auth cB],
HM [auth cB],
HO [auth dA],
HQ [auth dB],
IB [auth aA],
ID [auth aB],
IF [auth bA],
IG [auth bA],
IH [auth bB],
IJ [auth cA],
IK [auth cA],
IL [auth cB],
IO [auth dA],
IQ [auth dB],
IR [auth dL],
JB [auth aA],
JD [auth aB],
JE [auth aJ],
JF [auth bA],
JG [auth bA],
JH [auth bB],
JJ [auth cA],
JK [auth cA],
JL [auth cB],
JO [auth dA],
JQ [auth dB],
JR [auth dL],
KB [auth aA],
KD [auth aB],
KF [auth bA],
KG [auth bA],
KH [auth bB],
KJ [auth cA],
KK [auth cA],
KL [auth cB],
KN [auth dA],
KO [auth dA],
KQ [auth dB],
LB [auth aA],
LD [auth aB],
LF [auth bA],
LG [auth bA],
LH [auth bB],
LJ [auth cA],
LK [auth cA],
LL [auth cB],
LN [auth dA],
LO [auth dA],
LP [auth dB],
LQ [auth dB],
MB [auth aA],
MD [auth aB],
MF [auth bA],
MG [auth bA],
MH [auth bB],
MJ [auth cA],
MK [auth cA],
ML [auth cB],
MN [auth dA],
MO [auth dA],
MP [auth dB],
MQ [auth dB],
NB [auth aA],
ND [auth aB],
NE [auth aK],
NF [auth bA],
NG [auth bA],
NH [auth bB],
NI [auth bF],
NJ [auth cA],
NK [auth cA],
NL [auth cB],
NN [auth dA],
NO [auth dA],
NP [auth dB],
NQ [auth dB],
OB [auth aA],
OD [auth aB],
OF [auth bA],
OG [auth bA],
OH [auth bB],
OJ [auth cA],
OK [auth cA],
OL [auth cB],
ON [auth dA],
OO [auth dA],
OP [auth dB],
OQ [auth dB],
PB [auth aA],
PC [auth aB],
PD [auth aB],
PE [auth aK],
PF [auth bA],
PG [auth bA],
PH [auth bB],
PJ [auth cA],
PK [auth cA],
PL [auth cB],
PM [auth cF],
PN [auth dA],
PO [auth dA],
PP [auth dB],
PQ [auth dB],
QB [auth aA],
QD [auth aB],
QE [auth aK],
QF [auth bA],
QG [auth bA],
QH [auth bB],
QI [auth bF],
QJ [auth cA],
QK [auth cA],
QL [auth cB],
QN [auth dA],
QO [auth dA],
QP [auth dB],
RA [auth aA],
RB [auth aA],
RC [auth aB],
RD [auth aB],
RF [auth bA],
RH [auth bB],
RJ [auth cA],
RK [auth cA],
RL [auth cB],
RN [auth dA],
RO [auth dA],
RP [auth dB],
SA [auth aA],
SB [auth aA],
SC [auth aB],
SD [auth aB],
SF [auth bA],
SH [auth bB],
SJ [auth cA],
SL [auth cB],
SM [auth cF],
SN [auth dA],
SO [auth dA],
SP [auth dB],
TA [auth aA],
TB [auth aA],
TC [auth aB],
TD [auth aB],
TE [auth aL],
TF [auth bA],
TH [auth bB],
TI [auth bJ],
TJ [auth cA],
TL [auth cB],
TN [auth dA],
TO [auth dA],
TP [auth dB],
UA [auth aA],
UB [auth aA],
UC [auth aB],
UD [auth aB],
UE [auth aL],
UF [auth bA],
UH [auth bB],
UJ [auth cA],
UL [auth cB],
UM [auth cJ],
UN [auth dA],
UO [auth dA],
UP [auth dB],
VA [auth aA],
VB [auth aA],
VC [auth aB],
VD [auth aB],
VE [auth aL],
VF [auth bA],
VH [auth bB],
VJ [auth cA],
VL [auth cB],
VN [auth dA],
VO [auth dA],
VP [auth dB],
WA [auth aA],
WB [auth aA],
WC [auth aB],
WD [auth aB],
WF [auth bA],
WH [auth bB],
WJ [auth cA],
WL [auth cB],
WN [auth dA],
WO [auth dA],
WP [auth dB],
XA [auth aA],
XB [auth aA],
XC [auth aB],
XF [auth bA],
XH [auth bB],
XJ [auth cA],
XL [auth cB],
XN [auth dA],
XO [auth dA],
XP [auth dB],
XQ [auth dF],
YA [auth aA],
YB [auth aA],
YC [auth aB],
YF [auth bA],
YH [auth bB],
YI [auth bL],
YJ [auth cA],
YL [auth cB],
YM [auth cK],
YN [auth dA],
YO [auth dA],
YP [auth dB],
ZA [auth aA],
ZB [auth aA],
ZC [auth aB],
ZF [auth bA],
ZH [auth bB],
ZI [auth bL],
ZJ [auth cA],
ZL [auth cB],
ZN [auth dA],
ZO [auth dA],
ZP [auth dB]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0

Query on CL0


Download:Ideal Coordinates CCD File
BJ [auth cA],
JN [auth dA],
QA [auth aA],
ZE [auth bA]		CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG

Query on LMG


Download:Ideal Coordinates CCD File
BE [auth aB],
KI [auth bB],
MM [auth cB],
UQ [auth dB]		1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG


Download:Ideal Coordinates CCD File
IP [auth dA]
JP [auth dA]
NC [auth aA]
OC [auth aA]
YG [auth bA]
IP [auth dA],
JP [auth dA],
NC [auth aA],
OC [auth aA],
YG [auth bA],
YK [auth cA],
ZG [auth bA],
ZK [auth cA]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR

Query on BCR


Download:Ideal Coordinates CCD File
AE [auth aB]
AJ [auth bM]
BR [auth dI]
CN [auth cL]
CP [auth dA]
AE [auth aB],
AJ [auth bM],
BR [auth dI],
CN [auth cL],
CP [auth dA],
CR [auth dI],
DP [auth dA],
EP [auth dA],
ER [auth dJ],
FE [auth aF],
FP [auth dA],
FR [auth dJ],
GE [auth aF],
GN [auth cL],
GP [auth dA],
GR [auth dJ],
HI [auth bB],
HN [auth cL],
HP [auth dA],
HR [auth dL],
IC [auth aA],
IE [auth aI],
II [auth bB],
IN [auth cM],
JC [auth aA],
JI [auth bB],
JM [auth cB],
KC [auth aA],
KE [auth aJ],
KM [auth cB],
KR [auth dL],
LC [auth aA],
LE [auth aJ],
LM [auth cB],
LR [auth dM],
MC [auth aA],
ME [auth aJ],
OE [auth aK],
OI [auth bF],
PI [auth bF],
QM [auth cF],
RE [auth aK],
RI [auth bI],
RM [auth cF],
RQ [auth dB],
SE [auth aL],
SG [auth bA],
SI [auth bI],
SQ [auth dB],
TG [auth bA],
TK [auth cA],
TM [auth cI],
TQ [auth dB],
UG [auth bA],
UI [auth bJ],
UK [auth cA],
VG [auth bA],
VI [auth bJ],
VK [auth cA],
VM [auth cJ],
WE [auth aL],
WG [auth bA],
WI [auth bJ],
WK [auth cA],
WM [auth cJ],
XE [auth aL],
XG [auth bA],
XI [auth bL],
XK [auth cA],
XM [auth cJ],
YD [auth aB],
YE [auth aM],
YQ [auth dF],
ZD [auth aB],
ZM [auth cK],
ZQ [auth dF]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN

Query on PQN


Download:Ideal Coordinates CCD File
BP [auth dA]
GI [auth bB]
HC [auth aA]
IM [auth cB]
QQ [auth dB]
BP [auth dA],
GI [auth bB],
HC [auth aA],
IM [auth cB],
QQ [auth dB],
RG [auth bA],
SK [auth cA],
XD [auth aB]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4


Download:Ideal Coordinates CCD File
AH [auth bB]
BL [auth cB]
CE [auth aC]
DE [auth aC]
KP [auth dB]
AH [auth bB],
BL [auth cB],
CE [auth aC],
DE [auth aC],
KP [auth dB],
LI [auth bC],
MI [auth bC],
NM [auth cC],
OM [auth cC],
QC [auth aB],
VQ [auth dC],
WQ [auth dC]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13_2998
RECONSTRUCTIONRELION3

Structure Validation

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View more in-depth experimental data

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