9EYS | pdb_00009eys

Structure of Far-Red Photosystem I from C. thermalis PCC 7203

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Locating the missing chlorophylls f in far-red photosystem I.

Consoli, G., Tufail, F., Leong, H.F., Viola, S., Davis, G.A., Rew, N., Medranda, D., Hofer, M., Simpson, P., Sandrin, M., Chachuat, B., Nelson, J., Renger, T., Murray, J.W., Fantuzzi, A., Rutherford, A.W.

(2025) Science 390: eado6830-eado6830

  • DOI: https://doi.org/10.1126/science.ado6830
  • Primary Citation of Related Structures:  
    9EYS, 9I9L

  • PubMed Abstract: 

    The discovery of chlorophyll f-containing photosystems, with their long-wavelength photochemistry, represented a distinct, low-energy paradigm for oxygenic photosynthesis. Structural studies on chlorophyll f-containing photosystem I could identify some chlorophylls f sites, but none among the photochemically active pigments and concluded that chlorophyll f plays no photochemical role. Here, we report two cryo-EM structures of far-red PSI from Chroococcidiopsis thermalis PCC 7203, allowing the assignment of eight chlorophylls f molecules, including the redox active A -1B . Simulations of absorption difference spectra induced by charge separation indicate that the experimental spectra can be reproduced only by considering the presence of a chlorophyll f at the A -1B site. The chlorophyll f locations, wavelength assignments, and conserved far-red-specific residues provide functional insights for efficient use of long wavelength photons.

    • Organizational Affiliation: 
    • Department of Life Sciences, Imperial College, London, UK.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A,
M [auth N],
Y [auth a]		782Chroococcidiopsis thermalis PCC 7203Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for K9TWJ0 (Chroococcidiopsis thermalis (strain PCC 7203))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B,
N [auth O],
Z [auth b]		740Chroococcidiopsis thermalis PCC 7203Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for K9TVF3 (Chroococcidiopsis thermalis (strain PCC 7203))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerAA [auth c],
C,
O [auth P]		81Chroococcidiopsis thermalis PCC 7203Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for K9TVB5 (Chroococcidiopsis thermalis (strain PCC 7203))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIBA [auth d],
D,
P [auth Q]		142Chroococcidiopsis thermalis PCC 7203Mutation(s): 0 
Gene Names: Chro_4755
UniProt
Find proteins for K9U6S7 (Chroococcidiopsis thermalis (strain PCC 7203))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVCA [auth e],
E,
Q [auth R]		66Chroococcidiopsis thermalis PCC 7203Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIDA [auth f],
F,
R [auth S]		161Chroococcidiopsis thermalis PCC 7203Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIEA [auth g],
G [auth I],
S [auth T]		51Chroococcidiopsis thermalis PCC 7203Mutation(s): 0 
Gene Names: Chro_1016
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXFA [auth h],
H [auth J],
T [auth U]		46Chroococcidiopsis thermalis PCC 7203Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKGA [auth i],
I [auth K],
U [auth V]		80Chroococcidiopsis thermalis PCC 7203Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIHA [auth j],
J [auth L],
V [auth W]		183Chroococcidiopsis thermalis PCC 7203Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIIA [auth k],
K [auth M],
W [auth Y]		32Chroococcidiopsis thermalis PCC 7203Mutation(s): 0 
Gene Names: psaM, Chro_0108
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem one PsaXJA [auth l],
L [auth X],
X [auth Z]		29Chroococcidiopsis thermalis PCC 7203Mutation(s): 0 
Gene Names: Chro_0654
UniProt
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F6C (Subject of Investigation/LOI)
Query on F6C
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BE [auth B]
CF [auth L]
CI [auth O]
DO [auth b]
GJ [auth O]
BE [auth B],
CF [auth L],
CI [auth O],
DO [auth b],
GJ [auth O],
GK [auth W],
GN [auth b],
HB [auth A],
JB [auth A],
KO [auth b],
LA [auth A],
LG [auth N],
LP [auth j],
NG [auth N],
OC [auth A],
PF [auth N],
PL [auth a],
RH [auth N],
RL [auth a],
TK [auth a],
UD [auth B],
VM [auth a],
ZE [auth L],
ZI [auth O]
Chlorophyll F
C55 H68 Mg N4 O6
YUTLCKLMRUVWDE-FOFJUSMOSA-M
CLA (Subject of Investigation/LOI)
Query on CLA
Download Ideal Coordinates CCD File 
AB [auth A]
AD [auth B]
AE [auth B]
AF [auth L]
AG [auth N]
AB [auth A],
AD [auth B],
AE [auth B],
AF [auth L],
AG [auth N],
AH [auth N],
AI [auth O],
AJ [auth O],
AL [auth a],
AM [auth a],
AN [auth b],
AO [auth b],
BB [auth A],
BD [auth B],
BF [auth L],
BG [auth N],
BH [auth N],
BI [auth O],
BJ [auth O],
BL [auth a],
BM [auth a],
BN [auth b],
BO [auth b],
CB [auth A],
CD [auth B],
CE [auth B],
CG [auth N],
CH [auth N],
CJ [auth O],
CK [auth V],
CL [auth a],
CM [auth a],
CN [auth b],
CO [auth b],
DB [auth A],
DD [auth B],
DG [auth N],
DH [auth N],
DI [auth O],
DJ [auth O],
DK [auth V],
DL [auth a],
DM [auth a],
DN [auth b],
EB [auth A],
ED [auth B],
EG [auth N],
EI [auth O],
EJ [auth O],
EK [auth W],
EL [auth a],
EM [auth a],
EN [auth b],
EO [auth b],
FB [auth A],
FD [auth B],
FG [auth N],
FI [auth O],
FJ [auth O],
FK [auth W],
FL [auth a],
FM [auth a],
FN [auth b],
FO [auth b],
GB [auth A],
GD [auth B],
GG [auth N],
GI [auth O],
GL [auth a],
GM [auth a],
GO [auth b],
GP [auth i],
HD [auth B],
HG [auth N],
HI [auth O],
HJ [auth O],
HL [auth a],
HM [auth a],
HN [auth b],
HO [auth b],
HP [auth i],
IB [auth A],
ID [auth B],
IG [auth N],
II [auth O],
IL [auth a],
IN [auth b],
IO [auth b],
JD [auth B],
JG [auth N],
JI [auth O],
JL [auth a],
JN [auth b],
JO [auth b],
JP [auth j],
KB [auth A],
KD [auth B],
KG [auth N],
KI [auth O],
KL [auth a],
KN [auth b],
KP [auth j],
LB [auth A],
LD [auth B],
LI [auth O],
LL [auth a],
LN [auth b],
LO [auth b],
MA [auth A],
MB [auth A],
MD [auth B],
MG [auth N],
MI [auth O],
ML [auth a],
MN [auth b],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth B],
NF [auth X],
NI [auth O],
NL [auth a],
NN [auth b],
OA [auth A],
OB [auth A],
OD [auth B],
OE [auth F],
OG [auth N],
OI [auth O],
OL [auth a],
ON [auth b],
PA [auth A],
PB [auth A],
PD [auth B],
PG [auth N],
PI [auth O],
PN [auth b],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QF [auth N],
QG [auth N],
QI [auth O],
QL [auth a],
QN [auth b],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RF [auth N],
RG [auth N],
RI [auth O],
RK [auth Z],
RN [auth b],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SF [auth N],
SG [auth N],
SI [auth O],
SL [auth a],
SN [auth b],
TA [auth A],
TB [auth A],
TC [auth B],
TD [auth B],
TF [auth N],
TG [auth N],
TH [auth O],
TI [auth O],
TL [auth a],
TN [auth b],
UA [auth A],
UB [auth A],
UC [auth B],
UF [auth N],
UG [auth N],
UH [auth O],
UI [auth O],
UJ [auth S],
UK [auth a],
UL [auth a],
UN [auth b],
VA [auth A],
VB [auth A],
VC [auth B],
VD [auth B],
VF [auth N],
VG [auth N],
VH [auth O],
VI [auth O],
VK [auth a],
VL [auth a],
VN [auth b],
VP [auth l],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth B],
WF [auth N],
WG [auth N],
WH [auth O],
WI [auth O],
WK [auth a],
WL [auth a],
WN [auth b],
WO [auth f],
XA [auth A],
XB [auth A],
XC [auth B],
XD [auth B],
XE [auth K],
XF [auth N],
XG [auth N],
XH [auth O],
XI [auth O],
XK [auth a],
XL [auth a],
XM [auth b],
XN [auth b],
YA [auth A],
YB [auth A],
YC [auth B],
YD [auth B],
YE [auth K],
YF [auth N],
YG [auth N],
YH [auth O],
YI [auth O],
YK [auth a],
YL [auth a],
YM [auth b],
YN [auth b],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZD [auth B],
ZF [auth N],
ZG [auth N],
ZH [auth O],
ZK [auth a],
ZL [auth a],
ZM [auth b],
ZN [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0
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KA [auth A],
OF [auth N],
SK [auth a]		CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG
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AK [auth U]
CP [auth g]
EF [auth L]
EP [auth h]
IK [auth W]
AK [auth U],
CP [auth g],
EF [auth L],
EP [auth h],
IK [auth W],
KE [auth B],
MC [auth A],
NP [auth j],
QH [auth N],
QJ [auth O],
TE [auth I],
TO [auth b],
UM [auth a],
VE [auth J],
YJ [auth T]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG
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FF [auth L]
IC [auth A]
JK [auth W]
KF [auth M]
LF [auth X]
FF [auth L],
IC [auth A],
JK [auth W],
KF [auth M],
LF [auth X],
MF [auth X],
MH [auth N],
NK [auth Y],
OP [auth j],
PK [auth Z],
QK [auth Z],
QM [auth a],
RP [auth k],
TP [auth l],
UP [auth l]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR
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AP [auth g]
BK [auth V]
BP [auth g]
CC [auth A]
DC [auth A]
AP [auth g],
BK [auth V],
BP [auth g],
CC [auth A],
DC [auth A],
DF [auth L],
DP [auth h],
EC [auth A],
EE [auth B],
FC [auth A],
FE [auth B],
FP [auth i],
GC [auth A],
GE [auth B],
GH [auth N],
HC [auth A],
HE [auth B],
HF [auth L],
HH [auth N],
HK [auth W],
IE [auth B],
IH [auth N],
IP [auth j],
JE [auth B],
JF [auth M],
JH [auth N],
JJ [auth O],
KH [auth N],
KJ [auth O],
KM [auth a],
LH [auth N],
LJ [auth O],
LK [auth W],
LM [auth a],
MJ [auth O],
MM [auth a],
MP [auth j],
NJ [auth O],
NM [auth a],
NO [auth b],
OJ [auth O],
OK [auth Y],
OM [auth a],
OO [auth b],
PC [auth A],
PE [auth F],
PJ [auth O],
PM [auth a],
PO [auth b],
QE [auth F],
QO [auth b],
RE [auth I],
RO [auth b],
SE [auth I],
SH [auth N],
SO [auth b],
SP [auth k],
UE [auth J],
VJ [auth S],
WE [auth K],
WJ [auth T],
WM [auth a],
XJ [auth T],
XO [auth f],
YO [auth f],
ZJ [auth U]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT
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JC [auth A]
KC [auth A]
LC [auth A]
NH [auth N]
OH [auth N]
JC [auth A],
KC [auth A],
LC [auth A],
NH [auth N],
OH [auth N],
PH [auth N],
RM [auth a],
SM [auth a],
TM [auth a]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN
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AC [auth A]
DE [auth B]
EH [auth N]
IJ [auth O]
IM [auth a]
AC [auth A],
DE [auth B],
EH [auth N],
IJ [auth O],
IM [auth a],
MO [auth b]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4
Download Ideal Coordinates CCD File 
BC [auth A]
FH [auth N]
JM [auth a]
ME [auth C]
NE [auth C]
BC [auth A],
FH [auth N],
JM [auth a],
ME [auth C],
NE [auth C],
SJ [auth P],
TJ [auth P],
UO [auth c],
VO [auth c]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
LFA
Query on LFA
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GF [auth L]
KK [auth W]
LE [auth B]
PP [auth j]
RJ [auth O]
GF [auth L],
KK [auth W],
LE [auth B],
PP [auth j],
RJ [auth O],
ZO [auth f]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
IF [auth L],
MK [auth W],
QP [auth j]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/V002015/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R001383/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R00921X
Leverhulme TrustUnited KingdomRPG-2022-203

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-10-22
    Changes: Data collection, Database references
  • Version 1.2: 2025-12-24
    Changes: Data collection, Database references