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 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

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This is version 2.0 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 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 chlorophyll f sites, but none among the photochemically active pigments, and thus concluded that chlorophyll f plays no photochemical role. Here, we report two cryo-electron microscopy structures of far-red photosystem I from Chroococcidiopsis thermalis PCC 7203, allowing the assignment of eight chlorophyll f molecules, including the redox active A -1B . Simulations of absorption difference spectra induced by charge separation indicated 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.

Macromolecule Content 

  • Total Structure Weight: 1,111.57 kDa 
  • Atom Count: 75,954 
  • Modeled Residue Count: 6,924 
  • Deposited Residue Count: 7,179 
  • Unique protein chains: 12

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: psaA, Chro_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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Reference Sequence
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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: psaB, Chro_1018
EC: 1.97.1.12
UniProt
Find proteins for K9TVF3 (Chroococcidiopsis thermalis (strain PCC 7203))
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Reference Sequence
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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: psaC, Chro_0777
EC: 1.97.1.12
UniProt
Find proteins for K9TVB5 (Chroococcidiopsis thermalis (strain PCC 7203))
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Reference Sequence
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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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Reference Sequence
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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: psaE, Chro_2108
UniProt
Find proteins for K9TYF8 (Chroococcidiopsis thermalis (strain PCC 7203))
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Reference Sequence
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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
Find proteins for K9TZX8 (Chroococcidiopsis thermalis (strain PCC 7203))
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Reference Sequence
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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
Find proteins for K9TVX2 (Chroococcidiopsis thermalis (strain PCC 7203))
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Reference Sequence
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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
Find proteins for K9TYS7 (Chroococcidiopsis thermalis (strain PCC 7203))
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Reference Sequence
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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
Find proteins for K9TX25 (Chroococcidiopsis thermalis (strain PCC 7203))
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Reference Sequence
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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
Find proteins for K9TX29 (Chroococcidiopsis thermalis (strain PCC 7203))
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Reference Sequence
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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
Find proteins for K9TSY6 (Chroococcidiopsis thermalis (strain PCC 7203))
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Reference Sequence
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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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Reference Sequence

Small Molecules

Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F6C
(Subject of Investigation/LOI)

Query on F6C



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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

View Full Validation Report



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
  • Version 2.0: 2026-09-16
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary