9UH3 | pdb_00009uh3

PSI-9 FCPI supercomplex from haptophyte Chrysotila roscoffensis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9UH3

This is version 1.1 of the entry. See complete history

Literature

Multiple structures of photosystem I-FCPI supercomplexes from a coccolithophore alga reveal a modular antenna organization.

La Rocca, R.Tsai, P.C.Kato, K.Nakajima, Y.Akita, F.Shen, J.R.

(2026) Biochim Biophys Acta Bioenerg 1867: 149588-149588

  • DOI: https://doi.org/10.1016/j.bbabio.2026.149588
  • Primary Citation Related Structures: 
    9UH3, 9UH4, 9UNU, 9UOF, 9UOV

  • PubMed Abstract: 

    Photosystem I (PSI) converts light energy into chemical energy in photosynthesis, and forms supercomplexes with light-harvesting complexes (LHCI) in eukaryotes to enhance energy capture and transfer. Various numbers and organizations of both PSI core and LHCI subunits are observed in various organisms. A subgroup of haptophytes named coccolithophores play a major role in marine carbon cycle and CaCO 3 production, and the light-harvesting antennas of them are named FCPs (fucoxanthin-chlorophyll a/c binding protein) because they bind chlorophyll c and fucoxanthin in addition to chlorophyll a. A structure of a large PSI-FCPI supercomplex containing 38 FCPI subunits has been reported from a coccolithophore Emiliania huxleyi recently (L. Shen et al., Science 389, eadv2132, 2025). Here we solved five cryo-electron microscopy (cryo-EM) structures of PSI-FCPI supercomplexes isolated from another coccolithophore Chrysotila roscoffensis with different detergents at resolutions ranging from 2.3 to 1.7 Å. These structures represent discrete PSI-FCPIs containing 1, 4, 6, 8 and 9 FCPI subunits, with FCPIs arranged in a modular fashion. Association of each FCPI module to the PSI core, as well as the arrangement of protein subunits and pigments, are revealed. Contributions of individual antenna modules to excitation energy transfer were calculated and compared with PSI-FCPI supercomplexes from other species of coccolithophores and haptophytes. These results pinpoint the assembly of stable PSI-FCPI supercomplexes in C. roscoffensis and provide insights into how antenna modules contribute to energy transfer in coccolithophores.


  • Organizational Affiliation
    • Advanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.

Macromolecule Content 

  • Total Structure Weight: 669.76 kDa 
  • Atom Count: 42,258 
  • Modeled Residue Count: 3,643 
  • Deposited Residue Count: 4,198 
  • Unique protein chains: 21

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1 (psaA)752Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2 (psaB)734Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center (psaC)81Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II (psaD)142Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV (psaE)67Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III (psaF)184Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII (psaI)G [auth I]35Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IX (psaJ)H [auth J]39Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI (psaL)I [auth L]141Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XII (psaM)J [auth M]29Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c binding protein III (FCPI-3)K [auth O]201Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c binding protein VI (FCPI-6)L [auth P]231Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c binding protein IV (FCPI-4)M [auth Q]197Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaRN [auth R]90Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c binding protein II (FCPI-2)O [auth S]215Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c binding protein I (FCPI-1)P [auth U]191Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c binding protein VII (FCPI-7)Q [auth G]209Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c binding protein VIII (FCPI-8)R [auth H]169Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c binding protein IX (FCPI-9)S [auth K]200Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c binding protein V (FCPI-5)202Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaKU [auth k]89Chrysotila roscoffensisMutation(s): 0 

Small Molecules

Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
OD [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CL0

Query on CL0



Download:Ideal Coordinates CCD File
RB [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AE [auth F]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AE [auth F],
AF [auth O],
AI [auth U],
AJ [auth H],
AK [auth T],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BH [auth S],
BI [auth U],
BJ [auth H],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CF [auth O],
CJ [auth H],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DJ [auth H],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EJ [auth H],
EK [auth k],
FA [auth A],
FC [auth B],
FD [auth B],
FG [auth Q],
FH [auth S],
FI [auth G],
FK [auth k],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GG [auth Q],
GH [auth S],
GI [auth G],
HA [auth A],
HC [auth B],
HD [auth B],
HG [auth Q],
HH [auth S],
HI [auth G],
HJ [auth H],
IA [auth A],
IC [auth B],
IE [auth J],
IG [auth Q],
IH [auth S],
II [auth G],
JA [auth A],
JC [auth B],
JG [auth Q],
JI [auth G],
KA [auth A],
KC [auth B],
KG [auth Q],
KI [auth G],
KJ [auth K],
LA [auth A],
LC [auth B],
LE [auth L],
LG [auth Q],
LI [auth G],
LJ [auth K],
MA [auth A],
MC [auth B],
ME [auth L],
MI [auth G],
MJ [auth K],
NA [auth A],
NB [auth A],
NC [auth B],
NE [auth L],
NG [auth Q],
NI [auth G],
NJ [auth K],
OA [auth A],
OB [auth A],
OC [auth B],
OF [auth P],
OG [auth Q],
OI [auth G],
OJ [auth K],
PA [auth A],
PC [auth B],
PD [auth B],
PF [auth P],
PG [auth Q],
PH [auth S],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QF [auth P],
QH [auth S],
QJ [auth T],
RA [auth A],
RC [auth B],
RD [auth B],
RF [auth P],
RJ [auth T],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SF [auth P],
SG [auth Q],
SJ [auth T],
TA [auth A],
TB [auth A],
TC [auth B],
TE [auth O],
TI [auth G],
TJ [auth T],
UA [auth A],
UC [auth B],
UD [auth B],
UE [auth O],
UF [auth P],
UH [auth U],
UJ [auth T],
V [auth A],
VA [auth A],
VB [auth A],
VC [auth B],
VE [auth O],
VF [auth P],
VG [auth R],
VH [auth U],
VJ [auth T],
W [auth A],
WA [auth A],
WB [auth A],
WC [auth B],
WE [auth O],
WH [auth U],
WI [auth H],
WJ [auth T],
X [auth A],
XA [auth A],
XB [auth A],
XC [auth B],
XE [auth O],
XF [auth P],
XH [auth U],
XI [auth H],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth B],
YD [auth F],
YE [auth O],
YG [auth R],
YH [auth U],
YI [auth H],
YJ [auth T],
Z [auth A],
ZA [auth A],
ZC [auth B],
ZD [auth F],
ZE [auth O],
ZH [auth U],
ZI [auth H],
ZJ [auth T]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
(Subject of Investigation/LOI)

Query on SQD



Download:Ideal Coordinates CCD File
AH [auth S],
TD [auth B]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG

Query on LMG



Download:Ideal Coordinates CCD File
HE [auth J]
JF [auth P]
MH [auth S]
RH [auth U]
TG [auth Q]
HE [auth J],
JF [auth P],
MH [auth S],
RH [auth U],
TG [auth Q],
YF [auth P]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
HB [auth A],
IB [auth A],
IF [auth P],
UI [auth G]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86

Query on A86



Download:Ideal Coordinates CCD File
DG [auth Q]
LF [auth P]
QG [auth Q]
SH [auth U]
UG [auth Q]
DG [auth Q],
LF [auth P],
QG [auth Q],
SH [auth U],
UG [auth Q],
XG [auth R],
ZG [auth R]
(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate
C42 H58 O6
SJWWTRQNNRNTPU-XJUZQKKNSA-N
KC1

Query on KC1



Download:Ideal Coordinates CCD File
AG [auth P]
BF [auth O]
DI [auth U]
JH [auth S]
KF [auth P]
AG [auth P],
BF [auth O],
DI [auth U],
JH [auth S],
KF [auth P],
LH [auth S],
MG [auth Q],
NF [auth P],
TF [auth P],
XJ [auth T]
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
DD6

Query on DD6



Download:Ideal Coordinates CCD File
BG [auth P]
BK [auth T]
CI [auth U]
CK [auth T]
DF [auth O]
BG [auth P],
BK [auth T],
CI [auth U],
CK [auth T],
DF [auth O],
DH [auth S],
DK [auth k],
EF [auth O],
EG [auth Q],
EH [auth S],
EI [auth U],
FF [auth O],
FJ [auth H],
GE [auth J],
GF [auth O],
GJ [auth H],
KH [auth S],
MF [auth P],
NH [auth S],
OH [auth S],
PI [auth G],
PJ [auth K],
QI [auth G],
RG [auth Q],
RI [auth G],
SE [auth O],
SI [auth G],
TH [auth U],
VI [auth H],
WF [auth P],
ZF [auth P]
(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
C40 H54 O3
OGHZCSINIMWCSB-WMTIXGNLSA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
BE [auth F]
EE [auth I]
FE [auth I]
GK [auth k]
JB [auth A]
BE [auth F],
EE [auth I],
FE [auth I],
GK [auth k],
JB [auth A],
JD [auth B],
JE [auth J],
KB [auth A],
KD [auth B],
KE [auth L],
LB [auth A],
LD [auth B],
MB [auth A],
MD [auth B],
ND [auth B],
OE [auth L],
QE [auth M],
WG [auth R],
XD [auth F]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU

Query on LMU



Download:Ideal Coordinates CCD File
CE [auth F]
CG [auth P]
CH [auth S]
DE [auth F]
HF [auth O]
CE [auth F],
CG [auth P],
CH [auth S],
DE [auth F],
HF [auth O],
IJ [auth K],
JJ [auth K],
PB [auth A],
PE [auth L],
RE [auth M],
ZB [auth A]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN
(Subject of Investigation/LOI)

Query on PQN



Download:Ideal Coordinates CCD File
FB [auth A],
ID [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
(Subject of Investigation/LOI)

Query on SF4



Download:Ideal Coordinates CCD File
UB [auth A],
VD [auth C],
WD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-01
    Type: Initial release
  • Version 1.1: 2026-04-08
    Changes: Data collection, Database references