9I9L | pdb_00009i9l

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 
Gene Names: psaAChro_1019
EC: 1.97.1.12
UniProt
Find proteins for K9TWJ0 (Chroococcidiopsis thermalis (strain PCC 7203))
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UniProt GroupK9TWJ0
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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 
Gene Names: psaBChro_1018
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 
Gene Names: psaCChro_0777
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 
Gene Names: psaEChro_2108
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 
Gene Names: Chro_2236
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 
Gene Names: Chro_2235
UniProt
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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 
Gene Names: Chro_1412
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 
Gene Names: Chro_1017
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: psaMChro_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
Find proteins for K9TUG4 (Chroococcidiopsis thermalis (strain PCC 7203))
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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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AE [auth B]
AJ [auth O]
CF [auth L]
CO [auth b]
FF [auth L]
AE [auth B],
AJ [auth O],
CF [auth L],
CO [auth b],
FF [auth L],
GK [auth W],
HB [auth A],
HJ [auth O],
JB [auth A],
JK [auth W],
JO [auth b],
JP [auth j],
LA [auth A],
MP [auth j],
NC [auth A],
NG [auth N],
PG [auth N],
RF [auth N],
RL [auth a],
TD [auth B],
TH [auth N],
TL [auth a],
VK [auth a],
WM [auth a]
Chlorophyll F
C55 H68 Mg N4 O6
YUTLCKLMRUVWDE-FOFJUSMOSA-M
CLA
Query on CLA

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AB [auth A]
AD [auth B]
AF [auth K]
AG [auth N]
AH [auth N]
AB [auth A],
AD [auth B],
AF [auth K],
AG [auth N],
AH [auth N],
AI [auth O],
AL [auth a],
AM [auth a],
AN [auth b],
AO [auth b],
BB [auth A],
BD [auth B],
BE [auth B],
BF [auth K],
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],
CG [auth N],
CH [auth N],
CI [auth O],
CJ [auth O],
CL [auth a],
CM [auth a],
CN [auth b],
DB [auth A],
DD [auth B],
DF [auth L],
DG [auth N],
DH [auth N],
DI [auth O],
DJ [auth O],
DL [auth a],
DM [auth a],
DN [auth b],
DO [auth b],
EB [auth A],
ED [auth B],
EF [auth L],
EG [auth N],
EH [auth N],
EI [auth O],
EJ [auth O],
EK [auth V],
EL [auth a],
EM [auth a],
EN [auth b],
EO [auth b],
FB [auth A],
FD [auth B],
FG [auth N],
FH [auth N],
FI [auth O],
FJ [auth O],
FK [auth V],
FL [auth a],
FM [auth a],
FN [auth b],
FO [auth b],
GB [auth A],
GD [auth B],
GG [auth N],
GI [auth O],
GJ [auth O],
GL [auth a],
GM [auth a],
GN [auth b],
GO [auth b],
HD [auth B],
HG [auth N],
HI [auth O],
HK [auth W],
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],
IJ [auth O],
IK [auth W],
IL [auth a],
IM [auth a],
IN [auth b],
IO [auth b],
IP [auth i],
JD [auth B],
JG [auth N],
JI [auth O],
JL [auth a],
JM [auth a],
JN [auth b],
KB [auth A],
KD [auth B],
KG [auth N],
KI [auth O],
KL [auth a],
KN [auth b],
KO [auth b],
KP [auth j],
LB [auth A],
LD [auth B],
LG [auth N],
LI [auth O],
LL [auth a],
LN [auth b],
LP [auth j],
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],
ND [auth B],
NI [auth O],
NL [auth a],
NN [auth b],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OG [auth N],
OI [auth O],
OL [auth a],
ON [auth b],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth F],
PF [auth X],
PI [auth O],
PL [auth a],
PN [auth b],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QG [auth N],
QI [auth O],
QL [auth a],
QN [auth b],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RG [auth N],
RI [auth O],
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],
TF [auth N],
TG [auth N],
TI [auth O],
TK [auth Z],
TN [auth b],
UA [auth A],
UB [auth A],
UC [auth B],
UD [auth B],
UF [auth N],
UG [auth N],
UI [auth O],
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],
VJ [auth S],
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],
XA [auth A],
XB [auth A],
XC [auth B],
XD [auth B],
XF [auth N],
XG [auth N],
XH [auth O],
XI [auth O],
XK [auth a],
XL [auth a],
XM [auth b],
XN [auth b],
XO [auth f],
YA [auth A],
YB [auth A],
YC [auth B],
YD [auth B],
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],
ZI [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
Query on CL0

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KA [auth A],
QF [auth N],
UK [auth a]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG

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CK [auth U]
CP [auth g]
FP [auth h]
IF [auth L]
JE [auth B]
CK [auth U],
CP [auth g],
FP [auth h],
IF [auth L],
JE [auth B],
LE [auth B],
LK [auth W],
MC [auth A],
OP [auth j],
RJ [auth O],
SH [auth N],
TO [auth b],
VE [auth I],
YE [auth J],
ZJ [auth T]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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IC [auth A]
JF [auth L]
ME [auth B]
MK [auth W]
OF [auth X]
IC [auth A],
JF [auth L],
ME [auth B],
MK [auth W],
OF [auth X],
OH [auth N],
PP [auth j],
QK [auth Y],
SE [auth F],
SK [auth Z],
SM [auth a],
SP [auth k],
UH [auth N],
UP [auth l],
ZO [auth f]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR

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AK [auth U]
AP [auth g]
BK [auth U]
BP [auth g]
CC [auth A]
AK [auth U],
AP [auth g],
BK [auth U],
BP [auth g],
CC [auth A],
DC [auth A],
DE [auth B],
DK [auth V],
DP [auth h],
EC [auth A],
EE [auth B],
EP [auth h],
FC [auth A],
FE [auth B],
GC [auth A],
GE [auth B],
GF [auth L],
GP [auth i],
HC [auth A],
HE [auth B],
HF [auth L],
IE [auth B],
IH [auth N],
JH [auth N],
KH [auth N],
KJ [auth O],
KK [auth W],
LF [auth L],
LH [auth N],
LJ [auth O],
MH [auth N],
MJ [auth O],
MM [auth a],
MO [auth b],
NF [auth M],
NH [auth N],
NJ [auth O],
NM [auth a],
NO [auth b],
NP [auth j],
OJ [auth O],
OK [auth W],
OM [auth a],
OO [auth b],
PJ [auth O],
PM [auth a],
PO [auth b],
QE [auth F],
QJ [auth O],
QM [auth a],
QO [auth b],
RE [auth F],
RK [auth Y],
RM [auth a],
RO [auth b],
SO [auth b],
TE [auth I],
TP [auth k],
UE [auth I],
WE [auth J],
WJ [auth S],
XE [auth J],
XJ [auth T],
YJ [auth T],
YO [auth f],
ZE [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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JC [auth A]
KC [auth A]
LC [auth A]
PH [auth N]
QH [auth N]
JC [auth A],
KC [auth A],
LC [auth A],
PH [auth N],
QH [auth N],
RH [auth N],
TM [auth a],
UM [auth a],
VM [auth a]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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AC [auth A]
CE [auth B]
GH [auth N]
JJ [auth O]
KM [auth a]
AC [auth A],
CE [auth B],
GH [auth N],
JJ [auth O],
KM [auth a],
LO [auth b]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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BC [auth A]
HH [auth N]
LM [auth a]
NE [auth C]
OE [auth C]
BC [auth A],
HH [auth N],
LM [auth a],
NE [auth C],
OE [auth C],
TJ [auth P],
UJ [auth P],
VO [auth c],
WO [auth c]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
LFA
Query on LFA

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KE [auth B]
KF [auth L]
NK [auth W]
QP [auth j]
SJ [auth O]
KE [auth B],
KF [auth L],
NK [auth W],
QP [auth j],
SJ [auth O],
UO [auth b]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
CA
Query on CA

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MF [auth L],
PK [auth W],
RP [auth j]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.89 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: 2025-10-22
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Data collection, Database references