SMTL ID : 9lk4.1

Cryo-EM structure of Lhcb4.1-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana

Coordinates
PDB Format
Method
ELECTRON MICROSCOPY 3.10 Å
Oligo State
hetero-2-2-2-2-2-2-4-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-mer
Ligands
156 x CLA: CHLOROPHYLL A(Non-covalent)
4 x PHO: PHEOPHYTIN A(Non-covalent)
20 x BCR: BETA-CAROTENE(Non-covalent)
6 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)
8 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)
6 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)
2 x FE2: FE (II) ION(Non-covalent)
26 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)
2 x BCT: BICARBONATE ION(Non-functional Binders)
2 x 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(Non-covalent)
2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
52 x CHL: CHLOROPHYLL B(Non-covalent)
18 x LUT: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL(Non-covalent)
10 x NEX: (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(Non-covalent)
8 x XAT: (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(Non-covalent)
Links
RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP
Citation
Caferri, R. et al., A stress-induced paralog of Lhcb4 controls the photosystem II functional architecture in Arabidopsis thaliana. To Be Published
Release Date
2025-06-18
Peptides
Photosystem II protein D1: AW
Photosystem II CP47 reaction center protein: BX
Photosystem II CP43 reaction center protein: CY
Photosystem II D2 protein: DZ
Cytochrome b559 subunit alpha: E0
Cytochrome b559 subunit beta: F1
Chlorophyll a-b binding protein 2, chloroplastic: GN29
Photosystem II reaction center protein H: H3
Photosystem II reaction center protein I: I4
Photosystem II reaction center protein J: J5
Photosystem II reaction center protein K: K6
Photosystem II reaction center protein L: L7
Photosystem II reaction center protein M: M8
Oxygen-evolving enhancer protein 1-1, chloroplastic: Oa
Chlorophyll a-b binding protein CP29.1, chloroplastic: Pb
Photosystem II reaction center protein T: Qc
Photosystem II 5 kDa protein, chloroplastic: Rd
Photosystem II reaction center W protein, chloroplastic: Se
(thale cress) hypothetical protein: Tf
Chlorophyll a-b binding protein 2.2, chloroplastic: Ug
Photosystem II reaction center protein Z: Vh
Chlorophyll a-b binding protein CP26, chloroplastic: ij
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
W
a
B
B
X
b
C
C
Y
c
D
D
Z
d
E
E
0
e
F
F
1
f
G
G
N
N
2
g
9
n
H
H
3
h
I
I
4
i
J
J
5
j
K
K
6
k
L
L
7
l
M
M
8
m
O
O
a
o
P
R
b
r
Q
T
c
t
R
U
d
u
S
W
e
w
T
X
f
x
U
Y
g
y
V
Z
h
z
i
S
j
s
Membrane
We predict this structure to be a membrane protein.

Photosystem II protein D1

Toggle Identical (AW)

Photosystem II CP47 reaction center protein

Toggle Identical (BX)

Photosystem II CP43 reaction center protein

Toggle Identical (CY)

Photosystem II D2 protein

Toggle Identical (DZ)

Cytochrome b559 subunit alpha

Toggle Identical (E0)

Cytochrome b559 subunit beta

Toggle Identical (F1)

Chlorophyll a-b binding protein 2, chloroplastic

Toggle Identical (GN29)

Photosystem II reaction center protein H

Toggle Identical (H3)

Photosystem II reaction center protein I

Toggle Identical (I4)

Photosystem II reaction center protein J

Toggle Identical (J5)

Photosystem II reaction center protein K

Toggle Identical (K6)

Photosystem II reaction center protein L

Toggle Identical (L7)

Photosystem II reaction center protein M

Toggle Identical (M8)

Oxygen-evolving enhancer protein 1-1, chloroplastic

Toggle Identical (Oa)

Chlorophyll a-b binding protein CP29.1, chloroplastic

Toggle Identical (Pb)

Photosystem II reaction center protein T

Toggle Identical (Qc)

Photosystem II 5 kDa protein, chloroplastic

Toggle Identical (Rd)

Photosystem II reaction center W protein, chloroplastic

Toggle Identical (Se)

(thale cress) hypothetical protein

Toggle Identical (Tf)

Chlorophyll a-b binding protein 2.2, chloroplastic

Toggle Identical (Ug)

Photosystem II reaction center protein Z

Toggle Identical (Vh)

Chlorophyll a-b binding protein CP26, chloroplastic

Toggle Identical (ij)

Related Entries With Identical Sequence

3jcu.1 | 5mdx.1 | 7oui.1 | 8j6z.1 | 9lk5.1