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- PDB-9xk4: In situ C2S2M2L4-type PSII-LHCII supercomplex, core, protomer 2 -

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Basic information

Entry
Database: PDB / ID: 9xk4
TitleIn situ C2S2M2L4-type PSII-LHCII supercomplex, core, protomer 2
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 14
  • 23 kDa subunit of oxygen evolving system of photosystem II
  • 33 kDa subunit of oxygen evolving system of photosystem II
  • Os02g0581100 protein
  • Os07g0673550 protein
  • Os08g0119800 protein
KeywordsPHOTOSYNTHESIS / Photosystem II / C2S2M2L4-type / core / in situ / Oryza sativa / chloroplast
Function / homology
Function and homology information


chloroplast photosystem II / chloroplast thylakoid / photosystem II oxygen evolving complex / photosystem II assembly / thylakoid / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain ...chloroplast photosystem II / chloroplast thylakoid / photosystem II oxygen evolving complex / photosystem II assembly / thylakoid / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / photosystem II / extrinsic component of membrane / chlorophyll binding / plastid / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / calcium ion binding
Similarity search - Function
Photosystem II PsbR / Photosystem II PsbY, plant / Photosystem II 10 kDa polypeptide PsbR / Photosystem II 5kDa protein, chloroplastic / PsbP, C-terminal / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II protein Y (PsbY) ...Photosystem II PsbR / Photosystem II PsbY, plant / Photosystem II 10 kDa polypeptide PsbR / Photosystem II 5kDa protein, chloroplastic / PsbP, C-terminal / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II CP43 reaction centre protein / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II protein D1 / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / ALPHA-LINOLENIC ACID / Chem-MGE / CA-MN4-O5 CLUSTER ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / ALPHA-LINOLENIC ACID / Chem-MGE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein K / Photosystem II reaction center protein M / Photosystem II reaction center protein J / Photosystem II reaction center protein L / Photosystem II reaction center protein H / Photosystem II reaction center protein T / Photosystem II reaction center protein Z / Photosystem II protein D1 / Photosystem II D2 protein / Os02g0581100 protein / Photosystem II reaction center W protein, chloroplastic / Os08g0119800 protein / Os07g0673550 protein / 23 kDa subunit of oxygen evolving system of photosystem II / Photosystem II 10 kDa polypeptide, chloroplastic / 33 kDa subunit of oxygen evolving system of photosystem II
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsLi, J. / Elias, E. / Zhang, K. / Croce, R. / Zhu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32201038 China
CitationJournal: Nature / Year: 2026
Title: In situ structures of plant photosystem supercomplexes.
Authors: Jiao Li / Eduard Elias / Kai Zhang / Roberta Croce / Jiapeng Zhu /
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. 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.
History
DepositionNov 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1a: Photosystem II protein D1
1b: Photosystem II CP47 reaction center protein
1c: Photosystem II CP43 reaction center protein
1d: Photosystem II D2 protein
1e: Cytochrome b559 subunit alpha
1f: Cytochrome b559 subunit beta
1h: Photosystem II reaction center protein H
1i: Photosystem II reaction center protein I
1j: Photosystem II reaction center protein J
1k: Photosystem II reaction center protein K
1l: Photosystem II reaction center protein L
1m: Photosystem II reaction center protein M
1o: 33 kDa subunit of oxygen evolving system of photosystem II
1p: 23 kDa subunit of oxygen evolving system of photosystem II
1t: Photosystem II reaction center protein T
1u: Os02g0581100 protein
1v: Photosystem II 10 kDa polypeptide, chloroplastic
1w: Photosystem II reaction center W protein, chloroplastic
1x: Os07g0673550 protein
1y: Os08g0119800 protein
1z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,975115
Polymers302,29721
Non-polymers70,67994
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem II ... , 14 types, 14 molecules 1a1b1c1d1h1i1j1k1l1m1t1v1w1z

#1: Protein Photosystem II protein D1 / PSII D1 protein / Photosystem II Q(B) protein


Mass: 36845.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C434, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 55632.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C362
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 49289.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C365
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 38268.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C435, photosystem II
#7: Protein Photosystem II reaction center protein H / PSII-H / Photosystem II 10 kDa phosphoprotein


Mass: 6472.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C420
#8: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 3912.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C405
#9: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 3586.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C414
#10: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4273.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C408
#11: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4366.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C416
#12: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3783.538 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C411
#15: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3692.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C427
#17: Protein Photosystem II 10 kDa polypeptide, chloroplastic


Mass: 10861.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q8H4P7
#18: Protein/peptide Photosystem II reaction center W protein, chloroplastic / PSII 6.1 kDa protein


Mass: 4833.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q5ZBY9
#21: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6582.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C429

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Cytochrome b559 subunit ... , 2 types, 2 molecules 1e1f

#5: Protein Cytochrome b559 subunit alpha / PSII reaction center subunit V


Mass: 8654.690 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C368
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 3509.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P0C401

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Protein , 2 types, 2 molecules 1o1p

#13: Protein 33 kDa subunit of oxygen evolving system of photosystem II / 33 kDa thylakoid membrane protein / OEC 33 kDa subunit


Mass: 26609.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q943W1
#14: Protein 23 kDa subunit of oxygen evolving system of photosystem II / 23 kDa thylakoid membrane protein / OEC 23 kDa subunit


Mass: 20122.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q8GTK4

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Protein/peptide , 3 types, 3 molecules 1u1x1y

#16: Protein/peptide Os02g0581100 protein


Mass: 3009.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q0E032
#19: Protein/peptide Os07g0673550 protein / Ultraviolet-B-repressible protein / Photosystem II reaction centre X protein containing protein / expressed


Mass: 3927.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q7EXX2
#20: Protein/peptide Os08g0119800 protein / cDNA clone:001-024-H10 / full insert sequence / cDNA clone:J013109P06 / cDNA clone:J013136L01 / ...cDNA clone:001-024-H10 / full insert sequence / cDNA clone:J013109P06 / cDNA clone:J013136L01 / Os08g0119800 protein Photosystem II core complex proteins psbY / chloroplastic


Mass: 4061.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q6ZJ41

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Sugars , 1 types, 5 molecules

#31: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 13 types, 89 molecules

#22: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#23: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CaMn4O5 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O5 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical
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 / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C53H80O2 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical ChemComp-LNL / ALPHA-LINOLENIC ACID


Mass: 278.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H30O2 / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#34: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical ChemComp-MGE / (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE / MONOGALACTOSYL-DIACYLGLYCEROL


Mass: 688.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H72O10 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: In situ C2S2M2L4-type PSII-LHCII supercomplex, core, protomer 2
Type: COMPLEX / Entity ID: #10, #12-#14, #16-#17, #19-#21 / Source: NATURAL
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 1.375 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173752 / Symmetry type: POINT
RefinementHighest resolution: 2.78 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0199292
ELECTRON MICROSCOPYf_angle_d5.655139366
ELECTRON MICROSCOPYf_dihedral_angle_d15.77223729
ELECTRON MICROSCOPYf_chiral_restr0.22112953
ELECTRON MICROSCOPYf_plane_restr0.01416595

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