9KQQ | pdb_00009kqq

PSI-LHCI supercomplex binding with 8 Lhcas from C. subellipsoidea


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.0 of the entry. See complete history

Literature

Structural study of the chlorophyll between Lhca8 and PsaJ in an Antarctica green algal photosystem I-LHCI supercomplex revealed by its atomic structure.

Tsai, P.C.Kato, K.Shen, J.R.Akita, F.

(2025) Biochim Biophys Acta Bioenerg 1866: 149543-149543

  • DOI: https://doi.org/10.1016/j.bbabio.2025.149543
  • Primary Citation Related Structures: 
    9KQP, 9KQQ

  • PubMed Abstract: 

    Coccomyxa subellipsoidea is an oleaginous, non-motile unicellular green microalga isolated from Antarctica, and is an attractive candidate for CO 2 fixation and biomass production. C. subellipsoidea is the first polar green alga whose genome has been sequenced. Understanding the structure of photosystems from C. subellipsoidea can provide more information about the conversion of light energy into chemical energy under extreme environments. Photosystems I (PSI) is one of the two photosystems highly conserved from cyanobacteria to vascular plants, and associates with a large amount of outer light-harvesting complex (LHC) which absorb light energy and transfer them to the core complex. Here, we determined the structure of the PSI-10 LHCIs and PSI-8 LHCIs supercomplexes from C. subellipsoidea at 1.92 Å and 2.06 Å resolutions by cryo-electron microscopy, respectively. The supercomplex is similar to PSI-LHCI from other green algae, whereas a large amount of water molecules is observed in our structure because of the high-resolution map. Two novel chlorophylls (Chls), Chl a321 in Lhca4 and Chl a314 in Lhca8, are observed at the lumenal side in our structure, in which Lhca8-Chl a314 provides a potential excitation energy transfer (EET) pathway between the inner-belt of LHCI and the core at the lumenal side. A total of three major EET pathways from LHCIs to PSI core are proposed, and C. subellipsoidea might adapt to the extreme environment by transferring energy in these three different EET pathways instead of by two major pathways proposed in other organisms.


  • Organizational Affiliation
    • 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: 756.37 kDa 
  • Atom Count: 46,812 
  • Modeled Residue Count: 3,967 
  • Deposited Residue Count: 4,671 
  • Unique protein chains: 19

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1751Coccomyxa subellipsoidea C-169Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2734Coccomyxa subellipsoidea C-169Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Coccomyxa subellipsoidea C-169Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplastic192Coccomyxa subellipsoidea C-169Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction centre subunit IV/PsaE71Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III245Coccomyxa subellipsoidea C-169Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplastic138Coccomyxa subellipsoidea C-169Mutation(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 VIIIH [auth I]36Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E9NPX1 (Coccomyxa subellipsoidea (strain C-169))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXI [auth J]41Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI-KJ [auth K]131Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIK [auth M]31Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticL [auth a],
T [auth b]
229Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticM [auth 3]246Coccomyxa subellipsoidea C-169Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 4]246Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticO [auth 5]274Coccomyxa subellipsoidea C-169Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticP [auth 6]272Coccomyxa subellipsoidea C-169Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticQ [auth 7]259Coccomyxa subellipsoidea C-169Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticR [auth 8]255Coccomyxa subellipsoidea C-169Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI subunit VS [auth L]210Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence

Small Molecules

Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
(Subject of Investigation/LOI)

Query on DGD



Download:Ideal Coordinates CCD File
KC [auth B],
MJ [auth 7]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
(Subject of Investigation/LOI)

Query on CHL



Download:Ideal Coordinates CCD File
AB [auth A]
AC [auth A]
AD [auth B]
AE [auth B]
AH [auth 4]
AB [auth A],
AC [auth A],
AD [auth B],
AE [auth B],
AH [auth 4],
AI [auth 5],
AJ [auth 6],
AK [auth 7],
AL [auth 8],
BB [auth A],
BD [auth B],
BH [auth 4],
BI [auth 5],
BJ [auth 6],
BK [auth 7],
BL [auth 8],
CB [auth A],
CD [auth B],
CH [auth 4],
CI [auth 5],
CJ [auth 6],
CK [auth 7],
CL [auth 8],
DB [auth A],
DD [auth B],
DG [auth 3],
DH [auth 4],
DI [auth 5],
DJ [auth 6],
DK [auth 7],
DL [auth 8],
EB [auth A],
ED [auth B],
EG [auth 3],
EH [auth 4],
EI [auth 5],
EJ [auth 6],
EL [auth 8],
FB [auth A],
FD [auth B],
FG [auth 3],
FH [auth 4],
FI [auth 5],
FJ [auth 6],
GB [auth A],
GD [auth B],
GG [auth 3],
GH [auth 4],
GI [auth 5],
HB [auth A],
HD [auth B],
HG [auth 3],
HH [auth 4],
HI [auth 5],
HL [auth L],
IB [auth A],
ID [auth B],
IF [auth a],
IG [auth 3],
IH [auth 4],
II [auth 5],
IL [auth L],
JA [auth A],
JB [auth A],
JD [auth B],
JF [auth a],
JG [auth 3],
JH [auth 4],
KA [auth A],
KB [auth A],
KD [auth B],
KE [auth F],
KF [auth a],
KG [auth 3],
KH [auth 4],
KI [auth 5],
LA [auth A],
LB [auth A],
LD [auth B],
LE [auth F],
LF [auth a],
LG [auth 3],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
MF [auth a],
MG [auth 3],
ML [auth b],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NF [auth a],
NG [auth 3],
NL [auth b],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OF [auth a],
OG [auth 3],
OL [auth b],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PF [auth a],
PG [auth 3],
PK [auth 8],
PL [auth b],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QF [auth a],
QG [auth 3],
QI [auth 6],
QJ [auth 7],
QK [auth 8],
QL [auth b],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RF [auth a],
RI [auth 6],
RJ [auth 7],
RK [auth 8],
RL [auth b],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SE [auth J],
SF [auth a],
SH [auth 5],
SI [auth 6],
SJ [auth 7],
SK [auth 8],
SL [auth b],
TA [auth A],
TB [auth A],
TC [auth B],
TD [auth B],
TF [auth a],
TH [auth 5],
TI [auth 6],
TJ [auth 7],
TK [auth 8],
TL [auth b],
UA [auth A],
UB [auth A],
UC [auth B],
UD [auth B],
UF [auth a],
UG [auth 4],
UH [auth 5],
UI [auth 6],
UJ [auth 7],
UK [auth 8],
UL [auth b],
VA [auth A],
VB [auth A],
VC [auth B],
VD [auth B],
VF [auth a],
VG [auth 4],
VH [auth 5],
VI [auth 6],
VJ [auth 7],
VK [auth 8],
VL [auth b],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth B],
WE [auth K],
WG [auth 4],
WH [auth 5],
WI [auth 6],
WJ [auth 7],
WK [auth 8],
WL [auth b],
XA [auth A],
XB [auth A],
XC [auth B],
XD [auth B],
XE [auth K],
XG [auth 4],
XH [auth 5],
XI [auth 6],
XJ [auth 7],
XK [auth 8],
XL [auth b],
YA [auth A],
YB [auth A],
YC [auth B],
YD [auth B],
YE [auth K],
YG [auth 4],
YH [auth 5],
YI [auth 6],
YJ [auth 7],
YK [auth 8],
YL [auth b],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZD [auth B],
ZE [auth K],
ZG [auth 4],
ZH [auth 5],
ZI [auth 6],
ZJ [auth 7],
ZK [auth 8],
ZL [auth b]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CL0
(Subject of Investigation/LOI)

Query on CL0



Download:Ideal Coordinates CCD File
IA [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
SQD
(Subject of Investigation/LOI)

Query on SQD



Download:Ideal Coordinates CCD File
FK [auth 8]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
(Subject of Investigation/LOI)

Query on LMG



Download:Ideal Coordinates CCD File
CF [auth a],
GJ [auth 7],
LK [auth 8],
NE [auth J],
QE [auth J]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PTY
(Subject of Investigation/LOI)

Query on PTY



Download:Ideal Coordinates CCD File
QH [auth 5]PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
LHG
(Subject of Investigation/LOI)

Query on LHG



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DA [auth A]
EA [auth A]
FA [auth A]
GF [auth a]
HJ [auth 7]
DA [auth A],
EA [auth A],
FA [auth A],
GF [auth a],
HJ [auth 7],
JC [auth B],
JI [auth 5],
JK [auth 8],
KL [auth b],
LJ [auth 7],
PH [auth 5],
TG [auth 4]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
DGA
(Subject of Investigation/LOI)

Query on DGA



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KK [auth 8]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
XAT
(Subject of Investigation/LOI)

Query on XAT



Download:Ideal Coordinates CCD File
KJ [auth 7](3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
AXT
(Subject of Investigation/LOI)

Query on AXT



Download:Ideal Coordinates CCD File
EF [auth a]ASTAXANTHIN
C40 H52 O4
MQZIGYBFDRPAKN-UWFIBFSHSA-N
LUT
(Subject of Investigation/LOI)

Query on LUT



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AG [auth 3]
DF [auth a]
FE [auth F]
FF [auth a]
HK [auth 8]
AG [auth 3],
DF [auth a],
FE [auth F],
FF [auth a],
HK [auth 8],
IK [auth 8],
JJ [auth 7],
JL [auth b],
LL [auth b],
NH [auth 5],
NI [auth 6],
OH [auth 5],
OI [auth 6],
PE [auth J],
RG [auth 4],
SG [auth 4],
ZF [auth 3]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR
(Subject of Investigation/LOI)

Query on BCR



Download:Ideal Coordinates CCD File
AA [auth A]
BF [auth M]
DC [auth B]
DE [auth F]
EC [auth B]
AA [auth A],
BF [auth M],
DC [auth B],
DE [auth F],
EC [auth B],
FC [auth B],
FL [auth L],
GC [auth B],
GK [auth 8],
GL [auth L],
HC [auth B],
IC [auth B],
IJ [auth 7],
ME [auth I],
MH [auth 5],
MI [auth 6],
OE [auth J],
UE [auth K],
VE [auth K],
W [auth A],
WF [auth 3],
X [auth A],
XF [auth 3],
Y [auth A],
YF [auth 3],
Z [auth A]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
(Subject of Investigation/LOI)

Query on LMT



Download:Ideal Coordinates CCD File
BA [auth A]
CA [auth A]
EE [auth F]
LC [auth B]
LI [auth 5]
BA [auth A],
CA [auth A],
EE [auth F],
LC [auth B],
LI [auth 5],
NJ [auth 7],
RH [auth 5]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
(Subject of Investigation/LOI)

Query on PQN



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

Query on SF4



Download:Ideal Coordinates CCD File
BE [auth C],
CE [auth C],
V [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UNL(
Subject of Investigation/LOI)

Query on UNL



Download:Ideal Coordinates CCD File
AF [auth M]
BC [auth A]
BG [auth 3]
CG [auth 3]
EK [auth 7]
AF [auth M],
BC [auth A],
BG [auth 3],
CG [auth 3],
EK [auth 7],
GA [auth A],
GE [auth F],
HA [auth A],
HE [auth F],
HF [auth a],
IE [auth F],
JE [auth F],
LH [auth 4],
MK [auth 8],
NK [auth 8],
OJ [auth 7],
OK [auth 8],
PI [auth 6],
PJ [auth 7],
RE [auth J],
TE [auth K]
Unknown ligand
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP22H04916

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release