SMTL ID : 8c29.1

Cryo-EM structure of photosystem II C2S2 supercomplex from Norway spruce (Picea abies) at 2.8 Angstrom resolution

Coordinates
PDB Format
Method
ELECTRON MICROSCOPY
Oligo State
hetero-2-2-2-2-2-2-6-2-2-2-2-2-2-2-2-2-2-2-2-2-2-mer
Ligands
2 x FE2: FE (II) ION(Non-covalent)
154 x CLA: CHLOROPHYLL A(Non-covalent)
4 x PHO: PHEOPHYTIN A(Non-covalent)
20 x BCR: BETA-CAROTENE(Non-covalent)
4 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)
12 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)
12 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)
4 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)
18 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)
26 x LNL: ALPHA-LINOLENIC ACID(Non-covalent)(Non-functional Binders)
2 x PAM: PALMITOLEIC ACID(Non-covalent)
4 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)
2 x MG: MAGNESIUM ION(Non-covalent)
2 x VIV: (2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL(Non-covalent)
2 x BCT: BICARBONATE ION(Non-functional Binders)
2 x DGA: DIACYL GLYCEROL(Non-covalent)
2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
50 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
Opatikova, M. et al., Cryo-EM structure of a plant photosystem II supercomplex with light-harvesting protein Lhcb8 and alpha-tocopherol. Nat.Plants (2023)
Release Date
2023-07-26
Peptides
Photosystem II protein D1: AX
Photosystem II CP47 reaction center protein: BY
Photosystem II CP43 reaction center protein: CZ
Photosystem II D2 protein: D0
Cytochrome b559 subunit alpha: E1
Cytochrome b559 subunit beta: F2
Chlorophyll a-b binding protein, chloroplastic: GMV39i
Photosystem II reaction center protein H: H4
Photosystem II reaction center protein I: I5
Photosystem II reaction center protein K: J6
Photosystem II reaction center protein L: K7
Photosystem II reaction center protein M: L8
Oxygen-evolving enhancer protein 1, chloroplastic: Na
Chlorophyll a-b binding protein, chloroplastic: Ob
Chlorophyll a-b binding protein, chloroplastic: Pc
Photosystem II reaction center protein T: Qd
Photosystem II 5 kDa protein, chloroplastic: Re
Photosystem II reaction center protein Ycf12: Sf
PSII 6.1 kDa protein: Tg
Photosystem II PsbX: Uh
Photosystem II reaction center protein Z: Wj
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
X
a
B
B
Y
b
C
C
Z
c
D
D
0
d
E
E
1
e
F
F
2
f
G
G
M
N
V
Y
3
g
9
n
i
y
H
H
4
h
I
I
5
i
J
K
6
k
K
L
7
l
L
M
8
m
N
O
a
o
O
R
b
r
P
S
c
s
Q
T
d
t
R
U
e
u
S
V
f
v
T
W
g
w
U
X
h
x
W
Z
j
z
Membrane
We predict this structure to be a membrane protein.

Photosystem II protein D1

Toggle Identical (AX)

Photosystem II CP47 reaction center protein

Toggle Identical (BY)

Photosystem II CP43 reaction center protein

Toggle Identical (CZ)

Photosystem II D2 protein

Toggle Identical (D0)

Cytochrome b559 subunit alpha

Toggle Identical (E1)

Cytochrome b559 subunit beta

Toggle Identical (F2)

Chlorophyll a-b binding protein, chloroplastic

Toggle Identical (GMV39i)

Photosystem II reaction center protein H

Toggle Identical (H4)

Photosystem II reaction center protein I

Toggle Identical (I5)

Photosystem II reaction center protein K

Toggle Identical (J6)

Photosystem II reaction center protein L

Toggle Identical (K7)

Photosystem II reaction center protein M

Toggle Identical (L8)

Oxygen-evolving enhancer protein 1, chloroplastic

Toggle Identical (Na)

Chlorophyll a-b binding protein, chloroplastic

Toggle Identical (Ob)

Chlorophyll a-b binding protein, chloroplastic

Toggle Identical (Pc)

Photosystem II reaction center protein T

Toggle Identical (Qd)

Photosystem II 5 kDa protein, chloroplastic

Toggle Identical (Re)

Photosystem II reaction center protein Ycf12

Toggle Identical (Sf)

PSII 6.1 kDa protein

Toggle Identical (Tg)

Photosystem II PsbX

Toggle Identical (Uh)

Photosystem II reaction center protein Z

Toggle Identical (Wj)