9LK5 | pdb_00009lk5

The structure of Lhcb8-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

A stress-induced paralog of Lhcb4 controls the photosystem II functional architecture in Arabidopsis thaliana.

Caferri, R., Zhou, Q., Dall'Osto, L., Amelii, A., Shan, J., Liu, Z., Bassi, R.

(2025) Nat Commun 16: 6910-6910

  • DOI: https://doi.org/10.1038/s41467-025-62085-2
  • Primary Citation of Related Structures:  
    9LK4, 9LK5

  • PubMed Abstract: 

    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.

    • Organizational Affiliation: 
    • Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Verona, Italy.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
W [auth a]		353Arabidopsis thalianaMutation(s): 0 
EC: 1.10.3.9
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
X [auth b]		508Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P56777 (Arabidopsis thaliana)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
Y [auth c]		473Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
Z [auth d]		353Arabidopsis thalianaMutation(s): 0 
EC: 1.10.3.9
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaAA [auth e],
E		83Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaBA [auth f],
F		39Arabidopsis thalianaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 2, chloroplasticCA [auth g],
G,
N,
RA [auth n]		267Arabidopsis thalianaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HDA [auth h],
H		73Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IEA [auth i],
I		36Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JFA [auth j],
J		40Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KGA [auth k],
K		61Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LHA [auth l],
L		38Arabidopsis thalianaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MIA [auth m],
M		34Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 1-1, chloroplasticJA [auth o],
O		332Arabidopsis thalianaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein CP26, chloroplasticLA [auth s],
P [auth S]		280Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TMA [auth t],
Q [auth T]		33Arabidopsis thalianaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 5 kDa protein, chloroplasticNA [auth u],
R [auth U]		103Arabidopsis thalianaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center W protein, chloroplasticOA [auth w],
S [auth W]		133Arabidopsis thalianaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
(thale cress) hypothetical proteinPA [auth x],
T [auth X]		116Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 2.2, chloroplasticSA [auth y],
U [auth Y]		265Arabidopsis thalianaMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZQA [auth z],
V [auth Z]		62Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein CP29.3, chloroplasticKA [auth r],
TA [auth R]		286Arabidopsis thalianaMutation(s): 0 
Gene Names: LHCB4.3, At2g40100, F27I1.2
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Small Molecules
Ligands 17 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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AC [auth B]
BB [auth A]
CC [auth B]
GJ [auth d]
KD [auth D]
AC [auth B],
BB [auth A],
CC [auth B],
GJ [auth d],
KD [auth D],
PI [auth c],
UC [auth C],
ZH [auth b]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL
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AG [auth Y]
AM [auth n]
BL [auth s]
BM [auth n]
CL [auth s]
AG [auth Y],
AM [auth n],
BL [auth s],
BM [auth n],
CL [auth s],
DL [auth s],
EF [auth S],
EG [auth Y],
FG [auth Y],
GG [auth Y],
HG [auth Y],
IF [auth S],
IG [auth Y],
IJ [auth g],
IN [auth R],
JF [auth S],
JN [auth R],
KF [auth S],
KN [auth R],
LE [auth N],
LK [auth r],
MD [auth G],
MJ [auth g],
MK [auth r],
MM [auth y],
NJ [auth g],
NK [auth r],
OJ [auth g],
PE [auth N],
PJ [auth g],
QD [auth G],
QE [auth N],
QJ [auth g],
QM [auth y],
RD [auth G],
RE [auth N],
RM [auth y],
SD [auth G],
SE [auth N],
SM [auth y],
TD [auth G],
TE [auth N],
TL [auth n],
TM [auth y],
UD [auth G],
UM [auth y],
XK [auth s],
XL [auth n],
YL [auth n],
ZL [auth n]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA (Subject of Investigation/LOI)
Query on CLA
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AJ [auth d]
AL [auth s]
BD [auth D]
BG [auth Y]
BI [auth c]
AJ [auth d],
AL [auth s],
BD [auth D],
BG [auth Y],
BI [auth c],
CG [auth Y],
CI [auth c],
CM [auth n],
DB [auth B],
DD [auth D],
DG [auth Y],
DH [auth b],
DI [auth c],
DM [auth n],
EB [auth B],
ED [auth D],
EH [auth b],
EI [auth c],
EL [auth s],
EM [auth n],
EN [auth R],
FB [auth B],
FC [auth C],
FF [auth S],
FH [auth b],
FI [auth c],
FL [auth s],
FM [auth n],
FN [auth R],
GB [auth B],
GC [auth C],
GF [auth S],
GH [auth b],
GI [auth c],
GL [auth s],
GM [auth n],
GN [auth R],
HB [auth B],
HC [auth C],
HF [auth S],
HH [auth b],
HI [auth c],
HK [auth r],
HL [auth s],
HN [auth R],
IB [auth B],
IC [auth C],
IH [auth b],
II [auth c],
IK [auth r],
IL [auth s],
JB [auth B],
JC [auth C],
JG [auth Y],
JH [auth b],
JI [auth c],
JJ [auth g],
JK [auth r],
JL [auth s],
KB [auth B],
KC [auth C],
KG [auth Y],
KH [auth b],
KI [auth c],
KJ [auth g],
KK [auth r],
LB [auth B],
LC [auth C],
LF [auth S],
LG [auth Y],
LH [auth b],
LI [auth c],
LJ [auth g],
LN [auth R],
MB [auth B],
MC [auth C],
ME [auth N],
MF [auth S],
MG [auth Y],
MH [auth b],
MI [auth c],
MN [auth R],
NB [auth B],
NC [auth C],
ND [auth G],
NE [auth N],
NF [auth S],
NG [auth Y],
NH [auth b],
NI [auth c],
NM [auth y],
NN [auth R],
OB [auth B],
OC [auth C],
OD [auth G],
OE [auth N],
OF [auth S],
OH [auth b],
OK [auth r],
OM [auth y],
ON [auth R],
PB [auth B],
PC [auth C],
PD [auth G],
PF [auth S],
PH [auth b],
PK [auth r],
PM [auth y],
PN [auth R],
QB [auth B],
QC [auth C],
QF [auth S],
QH [auth b],
QK [auth r],
RB [auth B],
RC [auth C],
RH [auth b],
RJ [auth g],
RK [auth r],
SB [auth B],
SG [auth a],
SH [auth b],
SJ [auth g],
SK [auth r],
TJ [auth g],
UA [auth A],
UE [auth N],
UJ [auth g],
UL [auth n],
VA [auth A],
VD [auth G],
VE [auth N],
VG [auth a],
VJ [auth g],
VL [auth n],
VM [auth y],
WD [auth G],
WE [auth N],
WL [auth n],
WM [auth y],
XA [auth A],
XD [auth G],
XE [auth N],
XI [auth d],
XM [auth y],
YD [auth G],
YE [auth N],
YI [auth d],
YK [auth s],
YM [auth y],
ZD [auth G],
ZI [auth d],
ZK [auth s],
ZM [auth y]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
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CD [auth D],
TG [auth a],
UG [auth a],
WA [auth A]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD
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BC [auth B]
CH [auth b]
EK [auth l]
KE [auth L]
UI [auth c]
BC [auth B],
CH [auth b],
EK [auth l],
KE [auth L],
UI [auth c],
XG [auth a],
YC [auth C],
ZA [auth A]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG
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BH [auth b]
DF [auth S]
EC [auth C]
FJ [auth d]
JD [auth D]
BH [auth b],
DF [auth S],
EC [auth C],
FJ [auth d],
JD [auth D],
PL [auth s],
RL [auth w],
VI [auth c],
WB [auth B],
WH [auth b],
YF [auth W],
YG [auth a],
ZB [auth B],
ZC [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9
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CJ [auth d],
GD [auth D]		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
Query on LHG
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AI [auth b]
AK [auth g]
CF [auth N]
CN [auth y]
DC [auth B]
AI [auth b],
AK [auth g],
CF [auth N],
CN [auth y],
DC [auth B],
DJ [auth d],
EE [auth G],
EJ [auth d],
FK [auth l],
GK [auth l],
HD [auth D],
ID [auth D],
IE [auth L],
JE [auth L],
KM [auth n],
NL [auth s],
QI [auth c],
RG [auth Y],
RI [auth c],
TN [auth R],
UF [auth S],
VC [auth C],
WF [auth W],
WK [auth r],
XB [auth B],
XH [auth b],
YB [auth B],
YH [auth b]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM
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HJ [auth f],
LD [auth F]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NEX (Subject of Investigation/LOI)
Query on NEX
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BF [auth N]
DE [auth G]
DN [auth R]
JM [auth n]
ML [auth s]
BF [auth N],
DE [auth G],
DN [auth R],
JM [auth n],
ML [auth s],
QG [auth Y],
SN [auth R],
TF [auth S],
VK [auth r],
ZJ [auth g]
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
XAT (Subject of Investigation/LOI)
Query on XAT
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BK [auth g]
CE [auth G]
FE [auth G]
LM [auth y]
RN [auth R]
BK [auth g],
CE [auth G],
FE [auth G],
LM [auth y],
RN [auth R],
UK [auth r],
YJ [auth g],
ZF [auth Y]
(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
LUT (Subject of Investigation/LOI)
Query on LUT
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AE [auth G]
AF [auth N]
AN [auth y]
BE [auth G]
BN [auth y]
AE [auth G],
AF [auth N],
AN [auth y],
BE [auth G],
BN [auth y],
HM [auth n],
IM [auth n],
KL [auth s],
LL [auth s],
OG [auth Y],
PG [auth Y],
QN [auth R],
RF [auth S],
SF [auth S],
TK [auth r],
WJ [auth g],
XJ [auth g],
ZE [auth N]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR
Query on BCR
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BJ [auth d]
CK [auth h]
DK [auth k]
FD [auth D]
GE [auth H]
BJ [auth d],
CK [auth h],
DK [auth k],
FD [auth D],
GE [auth H],
HE [auth K],
OI [auth c],
SC [auth C],
SI [auth c],
SL [auth z],
TB [auth B],
TC [auth C],
TH [auth b],
UB [auth B],
UH [auth b],
VB [auth B],
VH [auth b],
WC [auth C],
WG [auth a],
YA [auth A]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
DMU
Query on DMU
Download Ideal Coordinates CCD File 
AD [auth C]
OL [auth s]
TI [auth c]
VF [auth S]
WI [auth c]
AD [auth C],
OL [auth s],
TI [auth c],
VF [auth S],
WI [auth c],
XC [auth C]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
VTQ
Query on VTQ
Download Ideal Coordinates CCD File 
QL [auth w],
XF [auth W]		RRR-ALPHA-TOCOPHERYLQUINONE
C29 H50 O3
LTVDFSLWFKLJDQ-IEOSBIPESA-N
BCT
Query on BCT
Download Ideal Coordinates CCD File 
AB [auth A],
ZG [auth a]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2
Download Ideal Coordinates CCD File 
AH [auth a],
CB [auth A]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--
National Natural Science Foundation of China (NSFC)China--
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Data collection, Database references
  • Version 1.2: 2025-08-13
    Changes: Data collection, Database references