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Biotechnology Information

8Z9D: cryo-EM structure of PSII-LHCII megacomplex from spinach

PDB ID:	8Z9D Download
MMDB ID:	254940
PDB Deposition Date:	2024/4/23
Updated in MMDB:	2024/11
Experimental Method:	electron microscopy
Resolution:	3.22 Å
Source Organism:	Spinacia oleracea
Similar Structures:

Biological Unit for 8Z9D: 112-meric; determined by author

Molecular Components in 8Z9D
Label	Count	Molecule
Proteins (112 molecules)
A a AA Aa	4	Photosystem II Protein D1
Oo O o OO	4	Oxygen-evolving Enhancer Protein 1, Chloroplastic
Rr R r RR	4	Chlorophyll A-B Binding Protein, Chloroplastic
Ss S s SS	4	Chlorophyll A-B Binding Protein, Chloroplastic
Tt T t TT	4	Photosystem II Reaction Center Protein T
Uu U u UU	4	Photosystem II 5 KDA Protein, Chloroplastic
Ww W w WW	4	Photosystem II Reaction Center W Protein, Chloroplastic
Xx X x XX	4	Photosystem II Reaction Center X Protein, Chloroplastic
Yy G N Y g n y GG NN YY Gg Nn	12	Chlorophyll A-B Binding Protein, Chloroplastic
Zz Z z ZZ	4	Photosystem II Reaction Center Protein Z
44 4	2	Chlorophyll A-B Binding Protein Cp24, Chloroplastic
Pp p P PP	4	Oxygen-evolving Enhancer Protein 2, Chloroplastic
Qq q Q QQ	4	Oxygen-evolving Enhancer Protein 3, Chloroplastic
11 22 1 2	4	Chlorophyll A-B Binding Protein, Chloroplastic
33 3	2	Chlorophyll A-B Binding Protein, Chloroplastic
0 00	2	Photosystem II 10 KDA Polypeptide, Chloroplastic
5 55	2	Photosystem II Reaction Center Proteins Psby, Chloroplastic
C c CC Cc	4	Photosystem II Cp43 Reaction Center Protein
D d DD Dd	4	Photosystem II D2 Protein
E e EE Ee	4	Cytochrome B559 Subunit Alpha
F f FF Ff	4	Cytochrome B559 Subunit Beta
H h HH Hh	4	Photosystem II Reaction Center Protein H
I i II Ii	4	Photosystem II Reaction Center Protein I
J j JJ Jj	4	Photosystem II Reaction Center Protein J
K k KK Kk	4	Photosystem II Reaction Center Protein K
L l LL Ll	4	Photosystem II Reaction Center Protein L
M m MM Mm	4	Photosystem II Reaction Center Protein M
b BB B Bb	4	Photosystem II Cp47 Reaction Center Protein
Chemicals and Non-standard biopolymers (781 molecules)
1	4	CA-MN4-O5 CLUSTER
2	4	FE (II) ION
3	8	CHLORIDE ION
4	374	CHLOROPHYLL A
5	8	PHEOPHYTIN A
6	44	BETA-CAROTENE
7	6	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
8	55	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
9	14	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
10	22	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
11	140	CHLOROPHYLL B
12	38	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
13	18	(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
14	14	(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
15	4	DODECYL-ALPHA-D-MALTOSIDE
16	20	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
17	4	BICARBONATE ION
18	4	PROTOPORPHYRIN IX CONTAINING FE