9LK4 image
Deposition Date 2025-01-16
Release Date 2025-06-18
Last Version Date 2025-08-13
Entry Detail
PDB ID:
9LK4
Keywords:
Title:
Cryo-EM structure of Lhcb4.1-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein D1
Gene (Uniprot):psbA
Chain IDs:A, W (auth: a)
Chain Length:353
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP47 reaction center protein
Gene (Uniprot):psbB
Chain IDs:B, X (auth: b)
Chain Length:508
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP43 reaction center protein
Gene (Uniprot):psbC
Chain IDs:C, Y (auth: c)
Chain Length:473
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein
Gene (Uniprot):psbD
Chain IDs:D, Z (auth: d)
Chain Length:353
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit alpha
Gene (Uniprot):psbE
Chain IDs:E, AA (auth: e)
Chain Length:83
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit beta
Gene (Uniprot):psbF
Chain IDs:F, BA (auth: f)
Chain Length:39
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Chlorophyll a-b binding protein 2, chloroplastic
Gene (Uniprot):LHCB1.1
Chain IDs:G, N, CA (auth: g), JA (auth: n)
Chain Length:267
Number of Molecules:4
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein H
Gene (Uniprot):psbH
Chain IDs:H, DA (auth: h)
Chain Length:73
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein I
Gene (Uniprot):psbI
Chain IDs:I, EA (auth: i)
Chain Length:36
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein J
Gene (Uniprot):psbJ
Chain IDs:J, FA (auth: j)
Chain Length:40
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein K
Gene (Uniprot):psbK
Chain IDs:K, GA (auth: k)
Chain Length:61
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein L
Gene (Uniprot):psbL
Chain IDs:L, HA (auth: l)
Chain Length:38
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein M
Gene (Uniprot):psbM
Chain IDs:M, IA (auth: m)
Chain Length:34
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Oxygen-evolving enhancer protein 1-1, chloroplastic
Gene (Uniprot):PSBO1
Chain IDs:O, KA (auth: o)
Chain Length:332
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Chlorophyll a-b binding protein CP29.1, chloroplastic
Gene (Uniprot):LHCB4.1
Chain IDs:P (auth: R), LA (auth: r)
Chain Length:300
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Chlorophyll a-b binding protein CP26, chloroplastic
Gene (Uniprot):LHCB5
Chain IDs:SA (auth: S), TA (auth: s)
Chain Length:280
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein T
Gene (Uniprot):psbT
Chain IDs:Q (auth: T), MA (auth: t)
Chain Length:33
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II 5 kDa protein, chloroplastic
Gene (Uniprot):PSBT
Chain IDs:R (auth: U), NA (auth: u)
Chain Length:103
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center W protein, chloroplastic
Gene (Uniprot):PSBW
Chain IDs:S (auth: W), OA (auth: w)
Chain Length:133
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:(thale cress) hypothetical protein
Gene (Uniprot):AT9943_LOCUS6465
Chain IDs:T (auth: X), PA (auth: x)
Chain Length:116
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Chlorophyll a-b binding protein 2.2, chloroplastic
Gene (Uniprot):LHCB2.2
Chain IDs:U (auth: Y), QA (auth: y)
Chain Length:265
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Z
Gene (Uniprot):psbZ
Chain IDs:V (auth: Z), RA (auth: z)
Chain Length:62
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Primary Citation
A stress-induced paralog of Lhcb4 controls the photosystem II functional architecture in Arabidopsis thaliana.
Nat Commun 16 6910 6910 (2025)
PMID: 40715075 DOI: 10.1038/s41467-025-62085-2

Abstact

Photosystem II (PSII) is the pigment-protein complex catalysing light-induced water oxidation. In Arabidopsis thaliana, it includes three Lhcb4-6 proteins linking the core complex to peripheral trimeric antennae. While Lhcb5 and Lhcb6 are encoded by single genes, Lhcb4 is encoded by three isoforms: Lhcb4.1 and Lhcb4.2, constitutively expressed, and Lhcb4.3 (Lhcb8), which accumulates under prolonged abiotic stress. Lhcb8 substitutes for Lhcb4, preventing Lhcb6 accumulation and resulting in a smaller PSII with high quantum yield. Cryo-electron microscopy reveals that Lhcb8 has a shorter carboxy-terminal domain, lacks two chlorophylls, and interacts more tightly with the PSII core, inducing structural changes in the PSII antenna system, ultimately inhibiting the formation of PSII arrays and favouring plastoquinone diffusion. We suggest that dynamic Lhcb4 vs Lhcb8 expression allows for PSII acclimation to contrasting light conditions, offering the potential for engineering crops with improved light use efficiency.

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