8f4i.1 | SWISS-MODEL Template Library

SMTL ID : 8f4i.1

RT XFEL structure of Photosystem II 2000 microseconds after the third illumination at 2.00 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

2 x OEX: CA-MN4-O5 CLUSTER(Covalent)

2 x OEY: CA-MN4-O6 CLUSTER(Covalent)

2 x FE2: FE (II) ION(Non-covalent)

4 x CL: CHLORIDE ION(Non-functional Binders)

70 x CLA: CHLOROPHYLL A(Non-covalent)

4 x PHO: PHEOPHYTIN A(Non-covalent)

22 x BCR: BETA-CAROTENE(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)

13 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)

8 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)

10 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)

31 x STE: STEARIC ACID(Non-covalent)(Non-functional Binders)

10 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

2 x BCT: BICARBONATE ION(Non-functional Binders)

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

2 x HEC: HEME C(Covalent)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Bhowmick, A. et al., Structural evidence for intermediates during O 2 formation in photosystem II. Nature (2023)

Release Date

2023-03-22

Peptides

Photosystem II protein D1 1: AU
Photosystem II CP47 reaction center protein: BV
Photosystem II CP43 reaction center protein: CW
Photosystem II D2 protein: DX
Cytochrome b559 subunit alpha: EY
Cytochrome b559 subunit beta: FZ
Photosystem II reaction center protein H: G0
Photosystem II reaction center protein I: H1
Photosystem II reaction center protein J: I2
Photosystem II reaction center protein K: J3
Photosystem II reaction center protein L: K4
Photosystem II reaction center protein M: L5
Photosystem II manganese-stabilizing polypeptide: M6
Photosystem II reaction center protein T: N7
Photosystem II 12 kDa extrinsic protein: O8
Cytochrome c-550: P9
Photosystem II reaction center protein Ycf12: Qa
Photosystem II reaction center X protein: Rb
Photosystem II reaction center protein Z: Sc
Photosystem II protein Y: Td

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

U
a

B
B

V
b

C
C

W
c

D
D

X
d

E
E

Y
e

F
F

Z
f

G
H

0
h

H
I

1
i

I
J

2
j

J
K

3
k

K
L

4
l

L
M

5
m

M
O

6
o

N
T

7
t

O
U

8
u

P
V

9
v

Q
Y

a
y

R
X

b
x

S
Z

c
z

T
R

d
r

Membrane

We predict this structure to be a membrane protein.
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Photosystem II protein D1 1

Toggle Identical (AU)

Photosystem II CP47 reaction center protein

Toggle Identical (BV)

Photosystem II CP43 reaction center protein

Photosystem II reaction center protein H

Photosystem II reaction center protein I

Toggle Identical (H1)

Photosystem II reaction center protein J

Toggle Identical (I2)

Photosystem II reaction center protein K

Toggle Identical (J3)

Photosystem II reaction center protein L

Photosystem II reaction center protein M

Photosystem II manganese-stabilizing polypeptide

Toggle Identical (M6)

Photosystem II reaction center protein T

Toggle Identical (N7)

Photosystem II 12 kDa extrinsic protein

Toggle Identical (O8)

Cytochrome c-550

Toggle Identical (P9)

Photosystem II reaction center protein Ycf12

Photosystem II reaction center X protein

Photosystem II reaction center protein Z

Toggle Identical (Sc)

Photosystem II protein Y

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