SMTL ID : 8ir9.1

XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 30-microsecond delay

Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.20 Å
Oligo State
hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-1-mer
Ligands
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)
8 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)
21 x GOL: GLYCEROL(Non-functional Binders)
2 x OEX: CA-MN4-O5 CLUSTER(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 UNL: UNKNOWN LIGAND(Non-covalent)(Non-functional Binders)
2 x BCT: BICARBONATE ION(Non-functional Binders)
10 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)
14 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
12 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)
11 x HTG: heptyl 1-thio-beta-D-glucopyranoside(Non-covalent)
8 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)
7 x CA: CALCIUM ION(Non-covalent)
2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
2 x MG: MAGNESIUM ION(Non-covalent)
2 x HEC: HEME C(Covalent)
Links
RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP
Citation
Li, H. et al., Oxygen-evolving photosystem II structures during S 1 -S 2 -S 3 transitions. Nature (2024)
Release Date
2024-01-17
Peptides
Photosystem II protein D1: AS
Photosystem II CP47 reaction center protein: BT
Photosystem II CP43 reaction center protein: CU
Photosystem II D2 protein: DV
Cytochrome b559 subunit alpha: EW
Cytochrome b559 subunit beta: FX
Photosystem II reaction center protein H: GY
Photosystem II reaction center protein I: HZ
Photosystem II reaction center protein J: I0
Photosystem II reaction center protein K: J1
Photosystem II reaction center protein L: K2
Photosystem II reaction center protein M: L3
Photosystem II manganese-stabilizing polypeptide: M4
Photosystem II reaction center protein T: N5
Photosystem II 12 kDa extrinsic protein: O6
Cytochrome c-550: P7
Photosystem II reaction center protein X: Q8
Photosystem II reaction center protein Ycf12: R9
Photosystem II reaction center protein Z: ac
Photosystem II protein Y: b
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
S
a
B
B
T
b
C
C
U
c
D
D
V
d
E
E
W
e
F
F
X
f
G
H
Y
h
H
I
Z
i
I
J
0
j
J
K
1
k
K
L
2
l
L
M
3
m
M
O
4
o
N
T
5
t
O
U
6
u
P
V
7
v
Q
X
8
x
R
Y
9
y
a
Z
c
z
b
R
Membrane
We predict this structure to be a membrane protein.

Photosystem II protein D1

Toggle Identical (AS)

Photosystem II CP47 reaction center protein

Toggle Identical (BT)

Photosystem II CP43 reaction center protein

Photosystem II D2 protein

Cytochrome b559 subunit alpha

Cytochrome b559 subunit beta

Photosystem II reaction center protein H

Toggle Identical (GY)

Photosystem II reaction center protein I

Toggle Identical (HZ)

Photosystem II reaction center protein J

Photosystem II reaction center protein K

Toggle Identical (J1)

Photosystem II reaction center protein L

Toggle Identical (K2)

Photosystem II reaction center protein M

Photosystem II manganese-stabilizing polypeptide

Toggle Identical (M4)

Photosystem II reaction center protein T

Toggle Identical (N5)

Photosystem II 12 kDa extrinsic protein

Cytochrome c-550

Toggle Identical (P7)

Photosystem II reaction center protein X

Toggle Identical (Q8)

Photosystem II reaction center protein Ycf12

Toggle Identical (R9)

Photosystem II reaction center protein Z

Toggle Identical (ac)

Photosystem II protein Y

Related Entries With Identical Sequence

1izl.1 | 1mz4.1 | 1s5l.1 | 1s5l.2 | 1w5c.1 | 1w5c.2 | 2axt.1 | 3a0b.1 | 3a0h.1 | 3kzi.1 | 3wu2.1 | 4fby.1 | 4il6.1 | 4ixq.1 | 4ixr.1 | 4pbu.1 | 4pj0.1 | 4rvy.1 | 4tnh.1 | 4tni.1 | 4tnj.1 | 4tnk.1 | 4ub6.1 | 4ub6.2 | 4ub8.1 | 4ub8.2 | 4v62.1 | 4v62.2 | 4v82.1 | 5b5e.1  more...