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Biotechnology Information

7D1U: Cryo-EM Structure of PSII at 2.08 angstrom resolution

PDB ID:	7D1U Download
MMDB ID:	200408
PDB Deposition Date:	2020/9/15
Updated in MMDB:	2025/08
Experimental Method:	electron microscopy
Resolution:	2.08 Å
Source Organism:	Thermostichus vulcanus
Similar Structures:

Biological Unit for 7D1U: 40-meric; determined by author

Molecular Components in 7D1U
Label	Count	Molecule
Proteins (40 molecules)
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	Photosystem II Manganese-stabilizing Polypeptide
T t	2	Photosystem II Reaction Center Protein T
U u	2	Photosystem II 12 KDA Extrinsic Protein
V v	2	Cytochrome C-550
Y y	2	Photosystem II Reaction Center Protein Ycf12
X x	2	Photosystem II Reaction Center Protein X
Z z	2	Photosystem II Reaction Center Protein Z
R r	2	Photosystem II Protein Y
Chemicals and Non-standard biopolymers (196 molecules)
1	2	CA-MN4-O5 CLUSTER
2	2	FE (II) ION
3	4	CHLORIDE ION
4	70	CHLOROPHYLL A
5	4	PHEOPHYTIN A
6	20	BETA-CAROTENE
7	8	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
8	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
9	36	UNKNOWN LIGAND
10	2	BICARBONATE ION
11	10	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
12	10	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
13	8	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
14	2	PROTOPORPHYRIN IX CONTAINING FE
15	2	(3R)-beta,beta-caroten-3-ol
16	8	DODECYL-BETA-D-MALTOSIDE
17	2	MAGNESIUM ION
18	2	HEME C