9XK7 | pdb_00009xk7

In situ C2S2M2L4-type PSII-LHCII supercomplex, strongly bound (S-) LHCII trimer with CP26, protomer 2

PDB DOI: https://doi.org/10.2210/pdb9XK7/pdb
EM Map EMD-66950: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Oryza sativa Japonica Group
Mutation(s): No

Deposited: 2025-11-05 Released: 2026-10-07
Deposition Author(s): Li, J., Elias, E., Zhang, K., Croce, R., Zhu, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.25 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

PubMed: 42527593 Search on PubMed Search on PubMed Central
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 ₂S ₂M ₂L 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: 153.26 kDa
Atom Count: 9,950
Modeled Residue Count: 874
Deposited Residue Count: 875
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein 2, chloroplastic	A [auth 09], B [auth 1g], C [auth 1n]	219	Oryza sativa Japonica Group	Mutation(s): 0
UniProt
Find proteins for P12331 (Oryza sativa subsp. japonica) Explore P12331 Go to UniProtKB: P12331
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12331
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein, chloroplastic	D [auth 1s]	218	Oryza sativa Japonica Group	Mutation(s): 0
UniProt
Find proteins for Q53N83 (Oryza sativa subsp. japonica) Explore Q53N83 Go to UniProtKB: Q53N83
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q53N83
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CHL (Subject of Investigation/LOI) Query on CHL Download:Ideal Coordinates CCD File SDF format, chain AA [auth 1g] SDF format, chain BA [auth 1g] SDF format, chain CA [auth 1g] SDF format, chain DA [auth 1g] SDF format, chain EA [auth 1g] SDF format, chain H [auth 09] SDF format, chain HB [auth 1s] SDF format, chain I [auth 09] SDF format, chain K [auth 09] SDF format, chain KB [auth 1s] SDF format, chain L [auth 09] SDF format, chain LB [auth 1s] SDF format, chain MB [auth 1s] SDF format, chain PA [auth 1n] SDF format, chain TA [auth 1n] SDF format, chain UA [auth 1n] SDF format, chain VA [auth 1n] SDF format, chain W [auth 1g] SDF format, chain WA [auth 1n] SDF format, chain XA [auth 1n] SDF format, chain J [auth 09] MOL2 format, chain AA [auth 1g] MOL2 format, chain BA [auth 1g] MOL2 format, chain CA [auth 1g] MOL2 format, chain DA [auth 1g] MOL2 format, chain EA [auth 1g] MOL2 format, chain H [auth 09] MOL2 format, chain HB [auth 1s] MOL2 format, chain I [auth 09] MOL2 format, chain K [auth 09] MOL2 format, chain KB [auth 1s] MOL2 format, chain L [auth 09] MOL2 format, chain LB [auth 1s] MOL2 format, chain MB [auth 1s] MOL2 format, chain PA [auth 1n] MOL2 format, chain TA [auth 1n] MOL2 format, chain UA [auth 1n] MOL2 format, chain VA [auth 1n] MOL2 format, chain W [auth 1g] MOL2 format, chain WA [auth 1n] MOL2 format, chain XA [auth 1n] MOL2 format, chain J [auth 09] mmCIF format, chain AA [auth 1g] mmCIF format, chain BA [auth 1g] mmCIF format, chain CA [auth 1g] mmCIF format, chain DA [auth 1g] mmCIF format, chain EA [auth 1g] mmCIF format, chain H [auth 09] mmCIF format, chain HB [auth 1s] mmCIF format, chain I [auth 09] mmCIF format, chain K [auth 09] mmCIF format, chain KB [auth 1s] mmCIF format, chain L [auth 09] mmCIF format, chain LB [auth 1s] mmCIF format, chain MB [auth 1s] mmCIF format, chain PA [auth 1n] mmCIF format, chain TA [auth 1n] mmCIF format, chain UA [auth 1n] mmCIF format, chain VA [auth 1n] mmCIF format, chain W [auth 1g] mmCIF format, chain WA [auth 1n] mmCIF format, chain XA [auth 1n] mmCIF format, chain J [auth 09]	AA [auth 1g] BA [auth 1g] CA [auth 1g] DA [auth 1g] EA [auth 1g] AA [auth 1g], BA [auth 1g], CA [auth 1g], DA [auth 1g], EA [auth 1g], H [auth 09], HB [auth 1s], I [auth 09], J [auth 09], K [auth 09], KB [auth 1s], L [auth 09], LB [auth 1s], MB [auth 1s], PA [auth 1n], TA [auth 1n], UA [auth 1n], VA [auth 1n], W [auth 1g], WA [auth 1n], XA [auth 1n]	CHLOROPHYLL B C₅₅ H₇₀ Mg N₄ O₆ MWVCRINOIIOUAU-UYSPMESUSA-M		Interactions Focus chain AA [auth 1g] Focus chain BA [auth 1g] Focus chain CA [auth 1g] Focus chain DA [auth 1g] Focus chain EA [auth 1g] Focus chain H [auth 09] Focus chain HB [auth 1s] Focus chain I [auth 09] Focus chain J [auth 09] Focus chain K [auth 09] Focus chain KB [auth 1s] Focus chain L [auth 09] Focus chain LB [auth 1s] Focus chain MB [auth 1s] Focus chain PA [auth 1n] Focus chain TA [auth 1n] Focus chain UA [auth 1n] Focus chain VA [auth 1n] Focus chain W [auth 1g] Focus chain WA [auth 1n] Focus chain XA [auth 1n] Interactions & Density Focus chain AA [auth 1g] Focus chain BA [auth 1g] Focus chain CA [auth 1g] Focus chain DA [auth 1g] Focus chain EA [auth 1g] Focus chain H [auth 09] Focus chain HB [auth 1s] Focus chain I [auth 09] Focus chain J [auth 09] Focus chain K [auth 09] Focus chain KB [auth 1s] Focus chain L [auth 09] Focus chain LB [auth 1s] Focus chain MB [auth 1s] Focus chain PA [auth 1n] Focus chain TA [auth 1n] Focus chain UA [auth 1n] Focus chain VA [auth 1n] Focus chain W [auth 1g] Focus chain WA [auth 1n] Focus chain XA [auth 1n]
CLA (Subject of Investigation/LOI) Query on CLA Download:Ideal Coordinates CCD File SDF format, chain AB [auth 1n] SDF format, chain BB [auth 1n] SDF format, chain CB [auth 1n] SDF format, chain E [auth 09] SDF format, chain F [auth 09] SDF format, chain FA [auth 1g] SDF format, chain G [auth 09] SDF format, chain GA [auth 1g] SDF format, chain HA [auth 1g] SDF format, chain IA [auth 1g] SDF format, chain IB [auth 1s] SDF format, chain JA [auth 1g] SDF format, chain JB [auth 1s] SDF format, chain M [auth 09] SDF format, chain N [auth 09] SDF format, chain NB [auth 1s] SDF format, chain O [auth 09] SDF format, chain OB [auth 1s] SDF format, chain P [auth 09] SDF format, chain PB [auth 1s] SDF format, chain QA [auth 1n] SDF format, chain QB [auth 1s] SDF format, chain RA [auth 1n] SDF format, chain RB [auth 1s] SDF format, chain SA [auth 1n] SDF format, chain SB [auth 1s] SDF format, chain TB [auth 1s] SDF format, chain U [auth 09] SDF format, chain X [auth 1g] SDF format, chain Y [auth 1g] SDF format, chain YA [auth 1n] SDF format, chain Z [auth 1g] SDF format, chain ZA [auth 1n] MOL2 format, chain AB [auth 1n] MOL2 format, chain BB [auth 1n] MOL2 format, chain CB [auth 1n] MOL2 format, chain E [auth 09] MOL2 format, chain F [auth 09] MOL2 format, chain FA [auth 1g] MOL2 format, chain G [auth 09] MOL2 format, chain GA [auth 1g] MOL2 format, chain HA [auth 1g] MOL2 format, chain IA [auth 1g] MOL2 format, chain IB [auth 1s] MOL2 format, chain JA [auth 1g] MOL2 format, chain JB [auth 1s] MOL2 format, chain M [auth 09] MOL2 format, chain N [auth 09] MOL2 format, chain NB [auth 1s] MOL2 format, chain O [auth 09] MOL2 format, chain OB [auth 1s] MOL2 format, chain P [auth 09] MOL2 format, chain PB [auth 1s] MOL2 format, chain QA [auth 1n] MOL2 format, chain QB [auth 1s] MOL2 format, chain RA [auth 1n] MOL2 format, chain RB [auth 1s] MOL2 format, chain SA [auth 1n] MOL2 format, chain SB [auth 1s] MOL2 format, chain TB [auth 1s] MOL2 format, chain U [auth 09] MOL2 format, chain X [auth 1g] MOL2 format, chain Y [auth 1g] MOL2 format, chain YA [auth 1n] MOL2 format, chain Z [auth 1g] MOL2 format, chain ZA [auth 1n] mmCIF format, chain AB [auth 1n] mmCIF format, chain BB [auth 1n] mmCIF format, chain CB [auth 1n] mmCIF format, chain E [auth 09] mmCIF format, chain F [auth 09] mmCIF format, chain FA [auth 1g] mmCIF format, chain G [auth 09] mmCIF format, chain GA [auth 1g] mmCIF format, chain HA [auth 1g] mmCIF format, chain IA [auth 1g] mmCIF format, chain IB [auth 1s] mmCIF format, chain JA [auth 1g] mmCIF format, chain JB [auth 1s] mmCIF format, chain M [auth 09] mmCIF format, chain N [auth 09] mmCIF format, chain NB [auth 1s] mmCIF format, chain O [auth 09] mmCIF format, chain OB [auth 1s] mmCIF format, chain P [auth 09] mmCIF format, chain PB [auth 1s] mmCIF format, chain QA [auth 1n] mmCIF format, chain QB [auth 1s] mmCIF format, chain RA [auth 1n] mmCIF format, chain RB [auth 1s] mmCIF format, chain SA [auth 1n] mmCIF format, chain SB [auth 1s] mmCIF format, chain TB [auth 1s] mmCIF format, chain U [auth 09] mmCIF format, chain X [auth 1g] mmCIF format, chain Y [auth 1g] mmCIF format, chain YA [auth 1n] mmCIF format, chain Z [auth 1g] mmCIF format, chain ZA [auth 1n]	AB [auth 1n] BB [auth 1n] CB [auth 1n] E [auth 09] F [auth 09] AB [auth 1n], BB [auth 1n], CB [auth 1n], E [auth 09], F [auth 09], FA [auth 1g], G [auth 09], GA [auth 1g], HA [auth 1g], IA [auth 1g], IB [auth 1s], JA [auth 1g], JB [auth 1s], M [auth 09], N [auth 09], NB [auth 1s], O [auth 09], OB [auth 1s], P [auth 09], PB [auth 1s], QA [auth 1n], QB [auth 1s], RA [auth 1n], RB [auth 1s], SA [auth 1n], SB [auth 1s], TB [auth 1s], U [auth 09], X [auth 1g], Y [auth 1g], YA [auth 1n], Z [auth 1g], ZA [auth 1n]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain AB [auth 1n] Focus chain BB [auth 1n] Focus chain CB [auth 1n] Focus chain E [auth 09] Focus chain F [auth 09] Focus chain FA [auth 1g] Focus chain G [auth 09] Focus chain GA [auth 1g] Focus chain HA [auth 1g] Focus chain IA [auth 1g] Focus chain IB [auth 1s] Focus chain JA [auth 1g] Focus chain JB [auth 1s] Focus chain M [auth 09] Focus chain N [auth 09] Focus chain NB [auth 1s] Focus chain O [auth 09] Focus chain OB [auth 1s] Focus chain P [auth 09] Focus chain PB [auth 1s] Focus chain QA [auth 1n] Focus chain QB [auth 1s] Focus chain RA [auth 1n] Focus chain RB [auth 1s] Focus chain SA [auth 1n] Focus chain SB [auth 1s] Focus chain TB [auth 1s] Focus chain U [auth 09] Focus chain X [auth 1g] Focus chain Y [auth 1g] Focus chain YA [auth 1n] Focus chain Z [auth 1g] Focus chain ZA [auth 1n] Interactions & Density Focus chain AB [auth 1n] Focus chain BB [auth 1n] Focus chain CB [auth 1n] Focus chain E [auth 09] Focus chain F [auth 09] Focus chain FA [auth 1g] Focus chain G [auth 09] Focus chain GA [auth 1g] Focus chain HA [auth 1g] Focus chain IA [auth 1g] Focus chain IB [auth 1s] Focus chain JA [auth 1g] Focus chain JB [auth 1s] Focus chain M [auth 09] Focus chain N [auth 09] Focus chain NB [auth 1s] Focus chain O [auth 09] Focus chain OB [auth 1s] Focus chain P [auth 09] Focus chain PB [auth 1s] Focus chain QA [auth 1n] Focus chain QB [auth 1s] Focus chain RA [auth 1n] Focus chain RB [auth 1s] Focus chain SA [auth 1n] Focus chain SB [auth 1s] Focus chain TB [auth 1s] Focus chain U [auth 09] Focus chain X [auth 1g] Focus chain Y [auth 1g] Focus chain YA [auth 1n] Focus chain Z [auth 1g] Focus chain ZA [auth 1n]
LHG (Subject of Investigation/LOI) Query on LHG Download:Ideal Coordinates CCD File SDF format, chain EB [auth 1n] SDF format, chain FB [auth 1n] SDF format, chain GB [auth 1s] SDF format, chain NA [auth 1g] SDF format, chain T [auth 09] SDF format, chain V [auth 09] SDF format, chain WB [auth 1s] MOL2 format, chain EB [auth 1n] MOL2 format, chain FB [auth 1n] MOL2 format, chain GB [auth 1s] MOL2 format, chain NA [auth 1g] MOL2 format, chain T [auth 09] MOL2 format, chain V [auth 09] MOL2 format, chain WB [auth 1s] mmCIF format, chain EB [auth 1n] mmCIF format, chain FB [auth 1n] mmCIF format, chain GB [auth 1s] mmCIF format, chain NA [auth 1g] mmCIF format, chain T [auth 09] mmCIF format, chain V [auth 09] mmCIF format, chain WB [auth 1s]	EB [auth 1n] FB [auth 1n] GB [auth 1s] NA [auth 1g] T [auth 09] EB [auth 1n], FB [auth 1n], GB [auth 1s], NA [auth 1g], T [auth 09], V [auth 09], WB [auth 1s]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain EB [auth 1n] Focus chain FB [auth 1n] Focus chain GB [auth 1s] Focus chain NA [auth 1g] Focus chain T [auth 09] Focus chain V [auth 09] Focus chain WB [auth 1s] Interactions & Density Focus chain EB [auth 1n] Focus chain FB [auth 1n] Focus chain GB [auth 1s] Focus chain NA [auth 1g] Focus chain T [auth 09] Focus chain V [auth 09] Focus chain WB [auth 1s]
XAT (Subject of Investigation/LOI) Query on XAT Download:Ideal Coordinates CCD File SDF format, chain MA [auth 1g] SDF format, chain OA [auth 1g] MOL2 format, chain MA [auth 1g] MOL2 format, chain OA [auth 1g] mmCIF format, chain MA [auth 1g] mmCIF format, chain OA [auth 1g]	MA [auth 1g], OA [auth 1g]	(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		Interactions Focus chain MA [auth 1g] Focus chain OA [auth 1g] Interactions & Density Focus chain MA [auth 1g] Focus chain OA [auth 1g]
LUT (Subject of Investigation/LOI) Query on LUT Download:Ideal Coordinates CCD File SDF format, chain DB [auth 1n] SDF format, chain KA [auth 1g] SDF format, chain LA [auth 1g] SDF format, chain Q [auth 09] SDF format, chain R [auth 09] SDF format, chain UB [auth 1s] SDF format, chain VB [auth 1s] MOL2 format, chain DB [auth 1n] MOL2 format, chain KA [auth 1g] MOL2 format, chain LA [auth 1g] MOL2 format, chain Q [auth 09] MOL2 format, chain R [auth 09] MOL2 format, chain UB [auth 1s] MOL2 format, chain VB [auth 1s] mmCIF format, chain DB [auth 1n] mmCIF format, chain KA [auth 1g] mmCIF format, chain LA [auth 1g] mmCIF format, chain Q [auth 09] mmCIF format, chain R [auth 09] mmCIF format, chain UB [auth 1s] mmCIF format, chain VB [auth 1s]	DB [auth 1n] KA [auth 1g] LA [auth 1g] Q [auth 09] R [auth 09] DB [auth 1n], KA [auth 1g], LA [auth 1g], Q [auth 09], R [auth 09], UB [auth 1s], VB [auth 1s]	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C₄₀ H₅₆ O₂ KBPHJBAIARWVSC-NSIPBSJQSA-N		Interactions Focus chain DB [auth 1n] Focus chain KA [auth 1g] Focus chain LA [auth 1g] Focus chain Q [auth 09] Focus chain R [auth 09] Focus chain UB [auth 1s] Focus chain VB [auth 1s] Interactions & Density Focus chain DB [auth 1n] Focus chain KA [auth 1g] Focus chain LA [auth 1g] Focus chain Q [auth 09] Focus chain R [auth 09] Focus chain UB [auth 1s] Focus chain VB [auth 1s]
VIV (Subject of Investigation/LOI) Query on VIV Download:Ideal Coordinates CCD File SDF format, chain S [auth 09] MOL2 format, chain S [auth 09] mmCIF format, chain S [auth 09]	S [auth 09]	(2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL C₂₉ H₅₀ O₂ GVJHHUAWPYXKBD-IEOSBIPESA-N		Interactions Focus chain S [auth 09] Interactions & Density Focus chain S [auth 09]