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5XNL: Structure of stacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum

PDB ID:	5XNL Download
MMDB ID:	154688
PDB Deposition Date:	2017/5/23
Updated in MMDB:	2022/11
Experimental Method:	electron microscopy
Resolution:	2.7 Å
Source Organism:	Pisum sativum
Similar Structures:

Biological Unit for 5XNL: 56-meric; determined by author

Molecular Components in 5XNL
Label	Count	Molecule
Proteins (56 molecules)
1 2 G N Y 5 6 g n y	10	Chlorophyll A-B Binding Protein 8, Chloroplastic
3 7	2	Chlorophyll A-B Binding Protein, Chloroplastic
4 8	2	Light Harvesting Chlorophyll A/b-binding Protein Lhcb6, Cp24
A a	2	Photosystem II Protein D1 (Gene symbol: psbA)
B b	2	Photosystem II Cp47 Reaction Center Protein
C c	2	Photosystem II Cp43 Reaction Center Protein (Gene symbol: psbC)
D d	2	Photosystem II D2 Protein (Gene symbol: psbD)
E e	2	Cytochrome B559 Subunit Alpha (Gene symbol: psbE)
F f	2	Cytochrome B559 Subunit Beta, Psbf
H h	2	Photosystem II Reaction Center Protein H
I i	2	Photosystem II Reaction Center Protein I, Psbi
J j	2	Photosystem II Reaction Center Protein J (Gene symbol: psbJ)
K k	2	Photosystem II Reaction Center Protein K
L l	2	Photosystem II Reaction Center Protein L (Gene symbol: psbL)
M m	2	Photosystem II Reaction Center Protein M (Gene symbol: psbM)
O o	2	Oxygen-evolving Enhancer Protein 1, Chloroplastic
P p	2	Oxygen-evolving Enhancer Protein 2, Chloroplastic
Q q	2	Oxygen-evolving Enhancer Protein 3
R r	2	Light Harvesting Chlorophyll A/b-binding Protein Lhcb4, Cp29
S s	2	Light Harvesting Chlorophyll A/b-binding Protein Lhcb5, Cp26
T t	2	Photosystem II Reaction Center Protein T (Gene symbol: psbT)
W w	2	Photosystem II Reaction Center Protein W
X x	2	Photosystem II Reaction Center Protein X
Z z	2	Photosystem II Reaction Center Protein Z (Gene symbol: psbZ)
Chemicals and Non-standard biopolymers (490 molecules)
1	98	CHLOROPHYLL B
2	216	CHLOROPHYLL A
3	32	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
4	16	(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
5	16	(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
6	36	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
7	24	BETA-CAROTENE
8	2	CA-MN4-O5 CLUSTER
9	2	FE (II) ION
10	4	CHLORIDE ION
11	4	PHEOPHYTIN A
12	8	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
13	14	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
14	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
15	10	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
16	2	BICARBONATE ION
17	2	PROTOPORPHYRIN IX CONTAINING FE