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8BD3: Cryo-EM structure of the Photosystem II - LHCII supercomplex from Chlorella ohadi

PDB ID:	8BD3 Download
MMDB ID:	233777
PDB Deposition Date:	2022/10/18
Updated in MMDB:	2023/08
Experimental Method:	electron microscopy
Resolution:	2.73 Å
Source Organism:	Chlorella ohadii
Similar Structures:

Biological Unit for 8BD3: 66-meric; determined by author

Molecular Components in 8BD3
Label	Count	Molecule
Proteins (66 molecules)
1 7	2	Chlorophyll A-B Binding Protein, Chloroplastic
2 4 G 9 q g	6	Chlorophyll A-B Binding Protein, Chloroplastic
3 5 N 8 p n	6	Chlorophyll A-B Binding of Lhcii
6 0	2	Chlorophyll A-B Binding of Lhcii
A a	2	Photosystem II Protein D1
B b	2	Photosystem II Cp47 Reaction Center Protein
C c	2	Photosystem II Cp43 Reaction Center Protein
D d	2	Photosystem II D2 Protein
E e	2	Cytochrome B559 Subunit Alpha
F f	2	Cytochrome B559 Subunit Beta
H h	2	Photosystem II Reaction Center Protein H
I i	2	Photosystem II Reaction Center Protein I
J j	2	Photosystem II Reaction Center Protein J
K k	2	Photosystem II Reaction Center Protein K
L l	2	Photosystem II Reaction Center Protein L
M m	2	Photosystem II Reaction Center Protein M
O o	2	Chloroplast Oxygen-evolving Enhancer Protein 1
R r	2	Chlorophyll a B Binding Cp29
S s	2	Chlorophyll a B-binding Cp26
T t	2	Photosystem II Reaction Center Protein T
V v	2	Photosystem II Reaction Center Protein Ycf12
W w	2	Photosystem II Reaction Center W Protein
X x	2	Photosystem II Reaction Center Protein X
Y y	2	Multifunctional Fusion Protein
Z z	2	Photosystem II Reaction Center Protein Z
U u	2	Chloroplast Oxygen-evolving Enhancer Protein 3
Q1 q1	2	Chloroplast Psby
P1 p1	2	Chloroplast Photosystem II 10 KDA Protein
F1 f1	2	Photosystem II Oxygen Evolving Enhancer 2
Chemicals and Non-standard biopolymers (672 molecules)
1	122	CHLOROPHYLL B
2	270	CHLOROPHYLL A
3	36	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
4	44	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
5	86	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
6	6	(3R)-beta,beta-caroten-3-ol
7	22	(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
8	8	(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
9	24	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
10	2	CA-MN4-O5 CLUSTER
11	2	FE (II) ION
12	4	CHLORIDE ION
13	4	PHEOPHYTIN A
14	22	BETA-CAROTENE
15	4	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
16	8	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
17	2	BICARBONATE ION
18	2	PROTOPORPHYRIN IX CONTAINING FE
19	4	DODECYL-ALPHA-D-MALTOSIDE