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SMTL ID : 7oui.1

Structure of C2S2M2-type Photosystem supercomplex from Arabidopsis thaliana (digitonin-extracted)

Coordinates
PDB Format
Method
ELECTRON MICROSCOPY
Oligo State
hetero-4-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-6-2-2-mer
Ligands
60 x CHL: CHLOROPHYLL B(Non-covalent)(Covalent)
162 x CLA: CHLOROPHYLL A(Non-covalent)(Covalent)
30 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)(Covalent)
4 x PHO: PHEOPHYTIN A(Non-covalent)
22 x BCR: BETA-CAROTENE(Non-covalent)(Covalent)
8 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)
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)
22 x AJP: Digitonin(Non-covalent)
2 x BCT: BICARBONATE ION(Non-functional Binders)
2 x FE2: FE (II) ION(Non-covalent)
8 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)
4 x CA: CALCIUM ION(Non-covalent)
2 x CL: CHLORIDE ION(Non-functional Binders)
2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(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)
2 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
Graca, A.T. et al., High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction. Sci Rep (2021)
Release Date
2021-08-18
Peptides
Lhcb1.4: AC02
Lhcb3.1: B1
Chlorophyll a-b binding protein, chloroplastic: D3
Photosystem II protein D1: E4
Photosystem II CP47 reaction center protein: F5
Photosystem II CP43 reaction center protein: G6
Photosystem II D2 protein: H7
Cytochrome b559 subunit alpha: I8
Cytochrome b559 subunit beta (PsbF): J9
Photosystem II reaction center protein H: Ka
Photosystem II reaction center protein I: Lb
Photosystem II reaction center protein K: Mc
Photosystem II reaction center protein L: Nd
Photosystem II reaction center protein M: Oe
Oxygen-evolving enhancer protein 1-1, chloroplastic: Pf
Photosystem II reaction center protein T: Qg
Photosystem II reaction center W protein, chloroplastic: Rh
PsbX: Si
Photosystem II reaction center protein Z: Tj
Chlorophyll a-b binding protein CP26, chloroplastic: Uk
Chlorophyll a-b binding protein 1, chloroplastic: VWXlmn
Chlorophyll a-b binding protein CP29.1, chloroplastic: Yo
PsbTn: Zp
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
1
C
3
0
5
2
7
B
2
1
6
D
4
3
8
E
A
4
a
F
B
5
b
G
C
6
c
H
D
7
d
I
E
8
e
J
F
9
f
K
H
a
h
L
I
b
i
M
K
c
k
N
L
d
l
O
M
e
m
P
O
f
o
Q
T
g
t
R
W
h
w
S
X
i
x
T
Z
j
z
U
S
k
s
V
G
W
N
X
Y
l
g
m
n
n
y
Y
R
o
r
Z
U
p
u
Membrane
We predict this structure to be a membrane protein.

Lhcb1.4

Toggle Identical (AC02)

Lhcb3.1

Toggle Identical (B1)

Chlorophyll a-b binding protein, chloroplastic

Toggle Identical (D3)

Photosystem II protein D1

Toggle Identical (E4)

Photosystem II CP47 reaction center protein

Toggle Identical (F5)

Photosystem II CP43 reaction center protein

Toggle Identical (G6)

Photosystem II D2 protein

Toggle Identical (H7)

Cytochrome b559 subunit alpha

Toggle Identical (I8)

Cytochrome b559 subunit beta (PsbF)

Toggle Identical (J9)

Photosystem II reaction center protein H

Toggle Identical (Ka)

Photosystem II reaction center protein I

Toggle Identical (Lb)

Photosystem II reaction center protein K

Toggle Identical (Mc)

Photosystem II reaction center protein L

Toggle Identical (Nd)

Photosystem II reaction center protein M

Toggle Identical (Oe)

Oxygen-evolving enhancer protein 1-1, chloroplastic

Toggle Identical (Pf)

Photosystem II reaction center protein T

Toggle Identical (Qg)

Photosystem II reaction center W protein, chloroplastic

Toggle Identical (Rh)

PsbX

Toggle Identical (Si)

Photosystem II reaction center protein Z

Toggle Identical (Tj)

Chlorophyll a-b binding protein CP26, chloroplastic

Toggle Identical (Uk)

Chlorophyll a-b binding protein 1, chloroplastic

Toggle Identical (Vl) Toggle Identical (Wm) Toggle Identical (Xn)

Chlorophyll a-b binding protein CP29.1, chloroplastic

Toggle Identical (Yo)

PsbTn

Toggle Identical (Zp)

Related Entries With Identical Sequence

3jcu.1 | 5mdx.1