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 21WI | pdb_000021wi

In situ structure of the trans-lumenal/trans-stromal PSII-LHCII trimer (TL-TS trimer) from Oryza sativa


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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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: 3,104.77 kDa 
  • Atom Count: 140,898 
  • Modeled Residue Count: 28,158 
  • Deposited Residue Count: 28,416 
  • Unique protein chains: 26

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 2, chloroplastic219Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: CAB2R, Os01g0600900, LOC_Os01g41710, OsJ_28992, P0518F01.17-1
UniProt
Find proteins for P12331 (Oryza sativa subsp. japonica)
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UniProt GroupP12331
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a/b-binding protein220Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for B7E6H8 (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, chloroplastic205Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Os04g0457000, OSNPB_040457000
UniProt
Find proteins for Q7XV11 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1334Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: psbA, PA001
EC: 1.10.3.9
UniProt
Find proteins for P0C432 (Oryza sativa)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center protein503Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: psbB, PA090
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UniProt GroupP0C362
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center protein450Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: psbC, PA019
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 protein341Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: psbD, PA018
EC: 1.10.3.9
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Find proteins for P0C435 (Oryza sativa)
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alpha75Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: psbE, PA079
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit beta36Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: psbF, PA078
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein H60Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: psbH, PA093
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Find proteins for P0C420 (Oryza sativa)
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein I34Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: psbI, PA012
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Find proteins for P0C405 (Oryza sativa)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein J35Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: psbJ
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Find proteins for P0C414 (Oryza sativa)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein K37Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: psbK, PA011
UniProt
Find proteins for P0C408 (Oryza sativa)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein L37Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: psbL
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein M33Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: psbM, PA029
UniProt
Find proteins for P0C411 (Oryza sativa)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
33 kDa subunit of oxygen evolving system of photosystem II248Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Os01g0501800, OSNPB_010501800
UniProt
Find proteins for Q943W1 (Oryza sativa subsp. japonica)
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
23 kDa subunit of oxygen evolving system of photosystem II186Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Os07g0141400, OSNPB_070141400
UniProt
Find proteins for Q8GTK4 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic234Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: RCABP69, Os07g0558400, OSNPB_070558400
UniProt
Find proteins for Q6Z411 (Oryza sativa subsp. japonica)
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic218Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: LOC_Os11g13890, Os11g0242800, OSNPB_110242800
UniProt
Find proteins for Q53N83 (Oryza sativa subsp. japonica)
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein T32Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: psbT
UniProt
Find proteins for P0C427 (Oryza sativa)
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Os02g0581100 protein27Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Os02g0581100, OSNPB_020581100
UniProt
Find proteins for Q0E032 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 10 kDa polypeptide, chloroplastic105Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: OJ1470_H06.117, Os07g0147500, OSNPB_070147500
UniProt
Find proteins for Q8H4P7 (Oryza sativa subsp. japonica)
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center W protein, chloroplastic54Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: PSBW, Os01g0773700, LOC_Os01g56680, P0490D09.17
UniProt
Find proteins for Q5ZBY9 (Oryza sativa subsp. japonica)
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Os07g0673550 protein39Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: P0470D12.144, Os07g0673550, P0304A10.1
UniProt
Find proteins for Q7EXX2 (Oryza sativa subsp. japonica)
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Os08g0119800 protein36Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Os08g0119800, OSNPB_080119800
UniProt
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Z62Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: psbZ
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

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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