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 9XK4 | pdb_00009xk4

In situ C2S2M2L4-type PSII-LHCII supercomplex, core, protomer 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9XK4

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: 372.98 kDa 
  • Atom Count: 25,527 
  • Modeled Residue Count: 2,724 
  • Deposited Residue Count: 2,749 
  • Unique protein chains: 21

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1A [auth 1a]333Oryza sativa Japonica GroupMutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for P0C434 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB [auth 1b]503Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for P0C362 (Oryza sativa)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC [auth 1c]450Oryza sativa Japonica GroupMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD [auth 1d]341Oryza sativa Japonica GroupMutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for P0C435 (Oryza sativa)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE [auth 1e]75Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for P0C368 (Oryza sativa)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF [auth 1f]31Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for P0C401 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth 1h]60Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for P0C420 (Oryza sativa)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth 1i]34Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for P0C405 (Oryza sativa)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JI [auth 1j]35Oryza sativa Japonica GroupMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KJ [auth 1k]37Oryza sativa Japonica GroupMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LK [auth 1l]37Oryza sativa Japonica GroupMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ML [auth 1m]34Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for P0C411 (Oryza sativa)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
33 kDa subunit of oxygen evolving system of photosystem IIM [auth 1o]248Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q943W1 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
23 kDa subunit of oxygen evolving system of photosystem IIN [auth 1p]186Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q8GTK4 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TO [auth 1t]32Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for P0C427 (Oryza sativa)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Os02g0581100 proteinP [auth 1u]27Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q0E032 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 10 kDa polypeptide, chloroplasticQ [auth 1v]105Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q8H4P7 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center W protein, chloroplasticR [auth 1w]44Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q5ZBY9 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Os07g0673550 proteinS [auth 1x]39Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q7EXX2 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Os08g0119800 proteinT [auth 1y]36Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q6ZJ41 (Oryza sativa subsp. japonica)
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZU [auth 1z]62Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for P0C429 (Oryza sativa)
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Reference Sequence

Small Molecules

Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
(Subject of Investigation/LOI)

Query on DGD



Download:Ideal Coordinates CCD File
CC [auth 1c],
DC [auth 1c],
EC [auth 1c],
FB [auth 1b],
JB [auth 1b]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
(Subject of Investigation/LOI)

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth 1a]
CA [auth 1a]
JA [auth 1b]
KA [auth 1b]
KC [auth 1d]
AA [auth 1a],
CA [auth 1a],
JA [auth 1b],
KA [auth 1b],
KC [auth 1d],
LA [auth 1b],
MA [auth 1b],
MB [auth 1c],
NA [auth 1b],
NB [auth 1c],
NC [auth 1d],
OA [auth 1b],
OB [auth 1c],
OC [auth 1d],
PA [auth 1b],
PB [auth 1c],
QA [auth 1b],
QB [auth 1c],
RA [auth 1b],
RB [auth 1c],
SA [auth 1b],
SB [auth 1c],
TA [auth 1b],
TB [auth 1c],
UA [auth 1b],
UB [auth 1c],
VA [auth 1b],
VB [auth 1c],
WA [auth 1b],
WB [auth 1c],
XA [auth 1b],
XB [auth 1c],
YA [auth 1b],
YB [auth 1c],
Z [auth 1a]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
(Subject of Investigation/LOI)

Query on PHO



Download:Ideal Coordinates CCD File
BA [auth 1a],
LC [auth 1d]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
(Subject of Investigation/LOI)

Query on SQD



Download:Ideal Coordinates CCD File
AC [auth 1c]
BC [auth 1c]
CB [auth 1b]
DB [auth 1b]
EA [auth 1a]
AC [auth 1c],
BC [auth 1c],
CB [auth 1b],
DB [auth 1b],
EA [auth 1a],
EB [auth 1b],
ED [auth 1l],
FA [auth 1a],
GA [auth 1a],
HD [auth 1w],
MC [auth 1d],
SC [auth 1d],
ZC [auth 1i]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
PL9
(Subject of Investigation/LOI)

Query on PL9



Download:Ideal Coordinates CCD File
HA [auth 1a],
RC [auth 1d],
TC [auth 1e],
WC [auth 1h]
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
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
(Subject of Investigation/LOI)

Query on LHG



Download:Ideal Coordinates CCD File
BD [auth 1j]
FC [auth 1c]
GB [auth 1b]
GC [auth 1c]
GD [auth 1v]
BD [auth 1j],
FC [auth 1c],
GB [auth 1b],
GC [auth 1c],
GD [auth 1v],
HB [auth 1b],
IA [auth 1a],
IB [auth 1b],
IC [auth 1d],
ID [auth 1w],
JC [auth 1d],
JD [auth 1w],
KB [auth 1b],
KD [auth 1w],
UC [auth 1e],
V [auth 1a]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
MGE
(Subject of Investigation/LOI)

Query on MGE



Download:Ideal Coordinates CCD File
CD [auth 1k](1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
C38 H72 O10
FIJGNIAJTZSERN-DQQGJSMTSA-N
HEM
(Subject of Investigation/LOI)

Query on HEM



Download:Ideal Coordinates CCD File
VC [auth 1f]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
(Subject of Investigation/LOI)

Query on BCR



Download:Ideal Coordinates CCD File
AB [auth 1b]
AD [auth 1j]
BB [auth 1b]
DA [auth 1a]
DD [auth 1k]
AB [auth 1b],
AD [auth 1j],
BB [auth 1b],
DA [auth 1a],
DD [auth 1k],
FD [auth 1t],
QC [auth 1d],
XC [auth 1h],
YC [auth 1i],
ZA [auth 1b],
ZB [auth 1c]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEX
(Subject of Investigation/LOI)

Query on OEX



Download:Ideal Coordinates CCD File
W [auth 1a]CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
LNL
(Subject of Investigation/LOI)

Query on LNL



Download:Ideal Coordinates CCD File
HC [auth 1c]ALPHA-LINOLENIC ACID
C18 H30 O2
DTOSIQBPPRVQHS-PDBXOOCHSA-N
BCT
(Subject of Investigation/LOI)

Query on BCT



Download:Ideal Coordinates CCD File
PC [auth 1d]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
(Subject of Investigation/LOI)

Query on FE2



Download:Ideal Coordinates CCD File
X [auth 1a]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
(Subject of Investigation/LOI)

Query on CL



Download:Ideal Coordinates CCD File
LB [auth 1c],
Y [auth 1a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 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