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 9XK9 | pdb_00009xk9

In situ C2S2M2L4-type PSII-LHCII supercomplex, moderately bound (M-) LHCII trimer with CP29 and CP24, protomer 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9XK9

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 657: 1094-1103

  • DOI: https://doi.org/10.1038/s41586-026-10847-3
  • Primary Citation Related Structures: 
    21WD, 21WG, 21WH, 21WI, 21WV, 27UR, 27UT, 9XJ1, 9XJ9, 9XK3, 9XK4, 9XK6, 9XK7, 9XK8, 9XK9

  • 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: 178.94 kDa 
  • Atom Count: 10,982 
  • Modeled Residue Count: 1,076 
  • Deposited Residue Count: 1,097 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 2, chloroplasticA [auth 05],
B [auth 06]
219Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for P12331 (Oryza sativa subsp. japonica)
Explore P12331 
Go to UniProtKB:  P12331
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12331
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a/b-binding proteinC [auth 07]220Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for B7E6H8 (Oryza sativa subsp. japonica)
Explore B7E6H8 
Go to UniProtKB:  B7E6H8
Entity Groups
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UniProt GroupB7E6H8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticD [auth 08]205Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q7XV11 (Oryza sativa subsp. japonica)
Explore Q7XV11 
Go to UniProtKB:  Q7XV11
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UniProt GroupQ7XV11
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticE [auth 1r]234Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q6Z411 (Oryza sativa subsp. japonica)
Explore Q6Z411 
Go to UniProtKB:  Q6Z411
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UniProt GroupQ6Z411
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHL
(Subject of Investigation/LOI)

Query on CHL



Download:Ideal Coordinates CCD File
GB [auth 1r]
HA [auth 07]
HB [auth 1r]
I [auth 05]
IA [auth 07]
GB [auth 1r],
HA [auth 07],
HB [auth 1r],
I [auth 05],
IA [auth 07],
IB [auth 1r],
J [auth 05],
JA [auth 07],
K [auth 05],
KA [auth 07],
L [auth 05],
PA [auth 07],
QB [auth 1r],
R [auth 05],
T [auth 05],
TA [auth 08],
U [auth 06],
UA [auth 08],
VA [auth 08],
W [auth 06],
WA [auth 08],
X [auth 06],
XA [auth 08],
Y [auth 06],
Z [auth 06]
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 06]
AB [auth 08]
BA [auth 06]
BB [auth 08]
CA [auth 06]
AA [auth 06],
AB [auth 08],
BA [auth 06],
BB [auth 08],
CA [auth 06],
CB [auth 08],
DA [auth 06],
DB [auth 08],
EA [auth 06],
EB [auth 08],
F [auth 05],
FA [auth 07],
FB [auth 1r],
G [auth 05],
GA [auth 07],
H [auth 05],
JB [auth 1r],
KB [auth 1r],
LA [auth 07],
LB [auth 1r],
M [auth 05],
MA [auth 07],
MB [auth 1r],
N [auth 05],
NA [auth 07],
NB [auth 1r],
O [auth 05],
OA [auth 07],
OB [auth 1r],
P [auth 05],
PB [auth 1r],
Q [auth 05],
QA [auth 07],
RB [auth 1r],
V [auth 06],
YA [auth 08],
ZA [auth 08]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LHG
(Subject of Investigation/LOI)

Query on LHG



Download:Ideal Coordinates CCD File
SA [auth 07],
UB [auth 1r]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT
(Subject of Investigation/LOI)

Query on XAT



Download:Ideal Coordinates CCD File
TB [auth 1r](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



Download:Ideal Coordinates CCD File
RA [auth 07],
S [auth 05],
SB [auth 1r]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.64 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)China32201038

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-07
    Type: Initial release