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Structure paper

TitleIn situ structures of plant photosystem supercomplexes.
Journal, issue, pagesNature, Vol. 657, Issue 8133, Page 1094-1103, Year 2026
Publish dateJul 29, 2026
AuthorsJiao Li / Eduard Elias / Kai Zhang / Roberta Croce / Jiapeng Zhu /
PubMed AbstractPhotosynthesis 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. Although ...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. 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 CSML-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.
External linksNature / PubMed:42527593 / PubMed Central
MethodsEM (single particle)
Resolution2.38 - 7.26 Å
Structure data

66925

9xj1

EMDB-66925, PDB-9xj1:
In situ structure of the PSI-LHCI supercomplex from Oryza sativa
Method: EM (single particle) / Resolution: 2.38 Å

66932

9xj9

EMDB-66932, PDB-9xj9:
In situ structure of the PSI-LHCI-LHCII supercomplex from Oryza sativa
Method: EM (single particle) / Resolution: 2.96 Å

66946

9xk3

EMDB-66946, PDB-9xk3:
In situ C2S2M2L4-type PSII-LHCII supercomplex, core, protomer 1
Method: EM (single particle) / Resolution: 2.7 Å

66947

9xk4

EMDB-66947, PDB-9xk4:
In situ C2S2M2L4-type PSII-LHCII supercomplex, core, protomer 2
Method: EM (single particle) / Resolution: 2.78 Å

66949

9xk6

EMDB-66949, PDB-9xk6:
In situ C2S2M2L4-type PSII-LHCII supercomplex, strongly bound (S-) LHCII trimer with CP26, protomer 1
Method: EM (single particle) / Resolution: 3.27 Å

66950

9xk7

EMDB-66950, PDB-9xk7:
In situ C2S2M2L4-type PSII-LHCII supercomplex, strongly bound (S-) LHCII trimer with CP26, protomer 2
Method: EM (single particle) / Resolution: 3.25 Å

66951

9xk8

EMDB-66951, PDB-9xk8:
In situ C2S2M2L4-type PSII-LHCII supercomplex, moderately bound (M-) LHCII trimer with CP29 and CP24, protomer 1
Method: EM (single particle) / Resolution: 3.59 Å

66952

9xk9

EMDB-66952, PDB-9xk9:
In situ C2S2M2L4-type PSII-LHCII supercomplex, moderately bound (M-) LHCII trimer with CP29 and CP24, protomer 2
Method: EM (single particle) / Resolution: 3.64 Å

EMDB-66971: In situ C2S2M2L4-type PSII-LHCII supercomplex, two loosely bound (L-) LHCII trimers at one side, protomer 1
Method: EM (single particle) / Resolution: 5.23 Å

EMDB-66974: In situ C2S2M2L4-type PSII-LHCII supercomplex, two loosely bound (L-) LHCII trimers at one side, protomer 2
Method: EM (single particle) / Resolution: 5.04 Å

68043

21wd

EMDB-68043, PDB-21wd:
In situ structure of the bis-trans-lumenal/trans-stromal PSII-LHCII tetramer (TL-TS-TL tetramer) from Oryza sativa
Method: EM (single particle) / Resolution: 4.24 Å

68047

21wg

EMDB-68047, PDB-21wg:
In situ structure of the mixed trans-lumenal/trans-stromal and side-by-side PSII-LHCII tetramer (TL-TS-SS tetramer) from Oryza sativa
Method: EM (single particle) / Resolution: 4.43 Å

68048

21wh

EMDB-68048, PDB-21wh:
In situ structure of the trans-stromal PSII-LHCII dimer(TS dimer) from Oryza sativa
Method: EM (single particle) / Resolution: 3.92 Å

68049

21wi

EMDB-68049, PDB-21wi:
In situ structure of the trans-lumenal/trans-stromal PSII-LHCII trimer (TL-TS trimer) from Oryza sativa
Method: EM (single particle) / Resolution: 4.27 Å

68060

21wv

EMDB-68060, PDB-21wv:
In situ structure of the C2S2M2L4-type PSII-LHCII supercomplex from Oryza sativa
Method: EM (single particle) / Resolution: 2.89 Å

EMDB-81432: In situ structure of side-by-side PSII-LHCII dimer (Consensus map)
Method: EM (single particle) / Resolution: 7.26 Å

EMDB-81433: In situ structure of side-by-side PSII-LHCII dimer (focused on PSII copy 1)
Method: EM (single particle) / Resolution: 4.27 Å

EMDB-81434: In situ structure of side-by-side PSII-LHCII dimer (focused on PSII copy 2)
Method: EM (single particle) / Resolution: 3.83 Å

81438

27ur

EMDB-81438, PDB-27ur:
In situ structure of the side-by-side PSII-LHCII dimer from Oryza sativa (composite)
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-81439: In situ structure of the trans-lumenal PSII-LHCII dimer (Consensus map)
Method: EM (single particle) / Resolution: 5.08 Å

EMDB-81440: In situ structure of the bis-trans-lumenal/trans-stromal PSII-LHCII tetramer (Consensus map)
Method: EM (single particle) / Resolution: 5.11 Å

EMDB-81441: In situ structure of the bis-trans-lumenal/trans-stromal PSII-LHCII tetramer (TL-TS-TL tetramer) (focused on PSII copy 1)
Method: EM (single particle) / Resolution: 4.11 Å

EMDB-81442: In situ structure of the bis-trans-lumenal/trans-stromal PSII-LHCII tetramer (TL-TS-TL tetramer) (focused on PSII copy 2)
Method: EM (single particle) / Resolution: 4.24 Å

EMDB-81443: In situ structure of the bis-trans-lumenal/trans-stromal PSII-LHCII tetramer (TL-TS-TL tetramer) (focused on PSII copy 3)
Method: EM (single particle) / Resolution: 3.48 Å

EMDB-81444: In situ structure of the trans-lumenal PSII-LHCII dimer (focused on PSII copy 1)
Method: EM (single particle) / Resolution: 4.34 Å

EMDB-81445: In situ structure of the bis-trans-lumenal/trans-stromal PSII-LHCII tetramer (TL-TS-TL tetramer) (focused on PSII copy 4)
Method: EM (single particle) / Resolution: 3.95 Å

EMDB-81446: In situ structure of the trans-lumenal PSII-LHCII dimer (focused on PSII copy 2)
Method: EM (single particle) / Resolution: 3.85 Å

81447

27ut

EMDB-81447, PDB-27ut:
In situ structure of the trans-lumenal PSII-LHCII dimer from Oryza sativa (composite)
Method: EM (single particle) / Resolution: 3.93 Å

EMDB-82229: In situ structure of the C2S2M2L4-typePSII-LHCII superconplex from Oryza sativa (consensus)
Method: EM (single particle) / Resolution: 3.48 Å

EMDB-82252: In situ structure of the trans-stromal PSII-LHCII dimer (Consensus map)
Method: EM (single particle) / Resolution: 5.98 Å

EMDB-82253: In situ structure of the trans-stromal PSII-LHCII dimer (focused on one PSII)
Method: EM (single particle) / Resolution: 3.92 Å

EMDB-82292: In situ structure of the trans-stromal PSII-LHCII dimer (focused on copy 2)
Method: EM (single particle) / Resolution: 3.53 Å

EMDB-82297: In situ structure of the trans-lumenal/trans-stromal PSII-LHCII trimer (Consensus)
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-82304: In situ structure of the trans-lumenal/trans-stromal PSII-LHCII trimer (focused on copy 1)
Method: EM (single particle) / Resolution: 4.07 Å

EMDB-82306: In situ structure of the trans-lumenal/trans-stromal PSII-LHCII trimer (focused on PSII copy 2)
Method: EM (single particle) / Resolution: 3.79 Å

EMDB-82307: In situ structure of the trans-lumenal/trans-stromal PSII-LHCII trimer (focused on PSII copy 3)
Method: EM (single particle) / Resolution: 4.27 Å

EMDB-82308: In situ structure of the mixed trans-lumenal/trans-stromal and side-by-side PSII-LHCII tetramer (Consensus map)
Method: EM (single particle) / Resolution: 3.49 Å

EMDB-82309: In situ structure of the mixed trans-lumenal/trans-stromal and side-by-side PSII-LHCII tetramer (Focused on PSII copy 1)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-82310: In situ structure of the mixed trans-lumenal/trans-stromal and side-by-side PSII-LHCII tetramer (Focused on PSII copy 2)
Method: EM (single particle) / Resolution: 4.43 Å

EMDB-82311: In situ structure of the mixed trans-lumenal/trans-stromal and side-by-side PSII-LHCII tetramer (Focused on PSII copy 3)
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-82312: In situ structure of the mixed trans-lumenal/trans-stromal and side-by-side PSII-LHCII tetramer (Focused on PSII copy 4)
Method: EM (single particle) / Resolution: 4.28 Å

Chemicals

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

ChemComp-CLA:
CHLOROPHYLL A

ChemComp-CHL:
CHLOROPHYLL B

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

ChemComp-VIV:
(2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

ChemComp-BCR:
BETA-CAROTENE

ChemComp-FE2:
Unknown entry

ChemComp-CL:
Unknown entry

ChemComp-PHO:
PHEOPHYTIN A

ChemComp-OEX:
CA-MN4-O5 CLUSTER

ChemComp-PL9:
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

ChemComp-MGE:
(1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE

ChemComp-LNL:
ALPHA-LINOLENIC ACID

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

ChemComp-XAT:
(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

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

ChemComp-PQN:
PHYLLOQUINONE

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-CL0:
CHLOROPHYLL A ISOMER

Source
  • Oryza sativa subsp. japonica (Japanese rice)
  • oryza sativa japonica group (Japanese rice)
  • Oryza sativa (Asian cultivated rice)
KeywordsPHOTOSYNTHESIS / Photosystem II / in situ / bis-trans-lumenal/trans-stromal PSII-LHCII tetramer / Oryza sativa / Chloroplast / TL-TS-SS tetramer / Trans-stromal PSII-LHCII dimer / trans-lumenal/trans-stromal PSII-LHCII / C2S2M2L4-type / side-by-side / trans-lumenal dimer / Photosystem I / PSI-LHCI / PSI-LHCI-LHCII / core / S-LHCII / CP26 / M-LHCII

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