9XJ9 | pdb_00009xj9

In situ structure of the PSI-LHCI-LHCII supercomplex from Oryza sativa


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

In situ structures of plant photosystem supercomplexes.

Li, J.Elias, E.Zhang, K.Croce, R.Zhu, J.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10847-3
  • Primary Citation Related Structures: 
    9XJ1, 9XJ9

  • PubMed Abstract: 

    Photosynthesis sustains life on Earth by converting light to chemical energy through the coordinated action of photosystem I (PSI) and photosystem II (PSII) within thylakoid membranes 1-4 . Although structures of isolated photosystems are available, their native organization in chloroplasts remains unknown. Here, using in situ cryo-electron microscopy, we directly imaged Oryza sativa (rice) chloroplasts and determined structures of photosystem supercomplexes in their native membrane environment. We resolved a C 2 S 2 M 2 L 4 -type PSII-light harvesting complex II (LHCII) supercomplex, including four LHCII antenna trimers that were not retained in purified preparations. Excitation energy transfer calculations based on this architecture closely reproduce in vivo measurements, indicating its physiological relevance. We also resolved asymmetric PSII-LHCII dimers, including side-by-side, trans-lumenal and trans-stromal architectures, and higher-order assemblies of trimers and tetramers. On the basis of these observations, we propose that PSII forms a trans-lumenal and trans-stromal 'skeleton' that shapes thylakoid morphology and supports grana stacking. In addition, we obtained high-resolution structures of PSI-LHCI-LHCII and PSI-LHCI supercomplexes. Together, these structures reveal extensive networks of lipids, pigments and cofactors, providing the first molecular framework for understanding how the native architecture of plant photosystem supports the exceptional photon-to-electron efficiency of photosynthesis.


  • Organizational Affiliation
    • Department of Cardiology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei, China. jiao.li@ustc.edu.cn.

Macromolecule Content 

  • Total Structure Weight: 686.58 kDa 
  • Atom Count: 43,745 
  • Modeled Residue Count: 4,096 
  • Deposited Residue Count: 4,097 
  • Unique protein chains: 20

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticA [auth 1]200Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q9ZSU0 (Oryza sativa)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticB [auth 2]207Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q6ZL95 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticC [auth 3]222Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q6H748 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll A-B binding proteinD [auth 4]198Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for B7EWI6 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1E [auth A]742Oryza sativa Japonica GroupMutation(s): 0 
EC: 1.97.1.12
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth B]732Oryza sativa Japonica GroupMutation(s): 0 
EC: 1.97.1.12
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerG [auth C]80Oryza sativa Japonica GroupMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for P0C359 (Oryza sativa)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplasticH [auth D]143Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q84PB4 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVI [auth E]66Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q6Z3V7 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIJ [auth F]158Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q8S7H8 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplasticK [auth G]97Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q652C4 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI, chloroplasticL [auth H]93Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q0DG05 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIM [auth I]30Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for P0C371 (Oryza sativa)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXN [auth J]44Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for P0C373 (Oryza sativa)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplasticO [auth K]88Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q84PB5 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI, chloroplasticP [auth L]163Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q2QSR5 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit N, chloroplasticQ [auth N]84Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for B8BNI3 (Oryza sativa subsp. indica)
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
H0622F05.3 proteinR [auth O]92Oryza sativa Japonica GroupMutation(s): 0 
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 1, chloroplasticS [auth X],
U [auth Z]
218Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for P12330 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticT [auth Y]222Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q10HD0 (Oryza sativa subsp. japonica)
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Reference Sequence

Small Molecules

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

Query on DGD



Download:Ideal Coordinates CCD File
GI [auth J],
UH [auth G],
VI [auth O],
ZG [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
(Subject of Investigation/LOI)

Query on CHL



Download:Ideal Coordinates CCD File
AC [auth 3]
FK [auth Y]
GJ [auth X]
HK [auth Z]
IK [auth Z]
AC [auth 3],
FK [auth Y],
GJ [auth X],
HK [auth Z],
IK [auth Z],
JJ [auth X],
JK [auth Z],
KA [auth 1],
KJ [auth X],
KK [auth Z],
LB [auth 2],
LJ [auth X],
LK [auth Z],
MJ [auth X],
NJ [auth X],
OC [auth 4],
PC [auth 4],
QC [auth 4],
RA [auth 2],
SA [auth 2],
SK [auth Z],
TB [auth 3],
V [auth 1],
VJ [auth Y],
WJ [auth Y],
XJ [auth Y],
YC [auth 4],
YJ [auth Y],
ZA [auth 2],
ZJ [auth Y]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
(Subject of Investigation/LOI)

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth 1]
AF [auth A]
AG [auth B]
AI [auth G]
AJ [auth O]
AA [auth 1],
AF [auth A],
AG [auth B],
AI [auth G],
AJ [auth O],
AK [auth Y],
BA [auth 1],
BC [auth 3],
BF [auth A],
BG [auth B],
BI [auth H],
BJ [auth O],
BK [auth Y],
CA [auth 1],
CC [auth 3],
CF [auth A],
CG [auth B],
CJ [auth O],
CK [auth Y],
DA [auth 1],
DC [auth 3],
DE [auth A],
DF [auth A],
DG [auth B],
DH [auth B],
DJ [auth O],
DK [auth Y],
EC [auth 3],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth B],
EH [auth B],
EI [auth J],
EJ [auth O],
EK [auth Y],
FC [auth 3],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth B],
FH [auth B],
FJ [auth X],
GC [auth 3],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth B],
GH [auth B],
GK [auth Y],
HB [auth 2],
HC [auth 3],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth B],
HH [auth B],
HJ [auth X],
IB [auth 2],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth B],
IH [auth B],
II [auth K],
IJ [auth X],
JB [auth 2],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth B],
JH [auth B],
JI [auth K],
KB [auth 2],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth B],
KH [auth B],
KI [auth K],
LA [auth 1],
LC [auth 4],
LD [auth A],
LE [auth A],
LF [auth B],
LG [auth B],
LH [auth B],
LI [auth K],
MA [auth 1],
MB [auth 2],
MC [auth 4],
MD [auth A],
ME [auth A],
MF [auth B],
MG [auth B],
MK [auth Z],
NA [auth 1],
NC [auth 4],
ND [auth A],
NE [auth A],
NF [auth B],
NG [auth B],
NK [auth Z],
OA [auth 1],
OE [auth A],
OF [auth B],
OG [auth B],
OJ [auth X],
OK [auth Z],
PA [auth 1],
PD [auth A],
PE [auth A],
PF [auth B],
PG [auth B],
PJ [auth X],
PK [auth Z],
QE [auth A],
QF [auth B],
QI [auth L],
QJ [auth X],
QK [auth Z],
RC [auth 4],
RE [auth A],
RF [auth B],
RG [auth B],
RI [auth L],
RJ [auth X],
RK [auth Z],
SC [auth 4],
SE [auth A],
SF [auth B],
SH [auth F],
SI [auth L],
TA [auth 2],
TC [auth 4],
TE [auth A],
TF [auth B],
TH [auth F],
TJ [auth Y],
TK [auth Z],
UA [auth 2],
UB [auth 3],
UC [auth 4],
UE [auth A],
UF [auth B],
UI [auth N],
UJ [auth Y],
UK [auth Z],
VA [auth 2],
VB [auth 3],
VC [auth 4],
VE [auth A],
VF [auth B],
W [auth 1],
WA [auth 2],
WB [auth 3],
WC [auth 4],
WE [auth A],
WF [auth B],
X [auth 1],
XA [auth 2],
XB [auth 3],
XC [auth 4],
XE [auth A],
XF [auth B],
Y [auth 1],
YA [auth 2],
YB [auth 3],
YE [auth A],
YF [auth B],
YH [auth G],
Z [auth 1],
ZB [auth 3],
ZC [auth 4],
ZE [auth A],
ZF [auth B],
ZH [auth G]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
(Subject of Investigation/LOI)

Query on CL0



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

Query on LHG



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AE [auth A]
AH [auth B]
BE [auth A]
BH [auth B]
DB [auth 2]
AE [auth A],
AH [auth B],
BE [auth A],
BH [auth B],
DB [auth 2],
EB [auth 2],
FB [auth 2],
GB [auth 2],
HA [auth 1],
IA [auth 1],
IC [auth 4],
JC [auth 4],
KC [auth 4],
OH [auth F],
QA [auth 1],
SB [auth 3],
SJ [auth X],
WH [auth G],
XD [auth A],
XH [auth G],
YD [auth A],
YI [auth O],
ZD [auth A],
ZI [auth O]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
MGE
(Subject of Investigation/LOI)

Query on MGE



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JA [auth 1]
QB [auth 3]
QH [auth F]
RB [auth 3]
RH [auth F]
JA [auth 1],
QB [auth 3],
QH [auth F],
RB [auth 3],
RH [auth F],
TI [auth N]
(1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
C38 H72 O10
FIJGNIAJTZSERN-DQQGJSMTSA-N
XAT
(Subject of Investigation/LOI)

Query on XAT



Download:Ideal Coordinates CCD File
BB [auth 2],
BD [auth 4],
FA [auth 1],
OB [auth 3]
(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
LUT
(Subject of Investigation/LOI)

Query on LUT



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AB [auth 2],
AD [auth 4],
DD [auth 4],
EA [auth 1],
NB [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



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CB [auth 2]
CD [auth 4]
CH [auth B]
CI [auth I]
DI [auth J]
CB [auth 2],
CD [auth 4],
CH [auth B],
CI [auth I],
DI [auth J],
FI [auth J],
GA [auth 1],
HI [auth K],
MI [auth L],
NI [auth L],
OI [auth L],
PB [auth 3],
PH [auth F],
PI [auth L],
RD [auth A],
SD [auth A],
SG [auth B],
TD [auth A],
TG [auth B],
UD [auth A],
UG [auth B],
VD [auth A],
VG [auth B],
VH [auth G],
WD [auth A],
WG [auth B],
WI [auth O],
XG [auth B],
XI [auth O],
YG [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
(Subject of Investigation/LOI)

Query on PQN



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

Query on SF4



Download:Ideal Coordinates CCD File
MH [auth C],
NH [auth C],
QD [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-12
    Type: Initial release