9M5A

cryo-EM structure of PSII D1-V185T from Thermosynechococcus vestitus BP-1

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, Q (A, a)	Photosystem II protein D1 3	polymer	360	39782.3	2	UniProt (Q8DIV4)	Thermosynechococcus vestitus BP-1	PSII D1 protein 3,Photosystem II Q(B) protein 3
2	B, R (B, b)	Photosystem II CP47 reaction center protein	polymer	510	56656.5	2	UniProt (Q8DIQ1)	Thermosynechococcus vestitus BP-1	PSII 47 kDa protein,Protein CP-47
3	C, S (C, c)	Photosystem II CP43 reaction center protein	polymer	461	50287.5	2	UniProt (Q8DIF8)	Thermosynechococcus vestitus BP-1	PSII 43 kDa protein,Protein CP-43
4	D, T (D, d)	Photosystem II D2 protein	polymer	352	39388.2	2	UniProt (Q8CM25)	Thermosynechococcus vestitus BP-1	PSII D2 protein,Photosystem II Q(A) protein
5	E, U (F, f)	Cytochrome b559 subunit beta	polymer	45	5067.9	2	UniProt (Q8DIN9)	Thermosynechococcus vestitus BP-1	PSII reaction center subunit VI
6	F, V (H, h)	Photosystem II reaction center protein H	polymer	66	7358.8	2	UniProt (Q8DJ43)	Thermosynechococcus vestitus BP-1	PSII-H
7	G, W (I, i)	Photosystem II reaction center protein I	polymer	38	4438.3	2	UniProt (Q8DJZ6)	Thermosynechococcus vestitus BP-1	PSII-I,PSII 4.4 kDa protein
8	H, X (J, j)	Photosystem II reaction center protein J	polymer	40	4105.9	2	UniProt (P59087)	Thermosynechococcus vestitus BP-1	PSII-J
9	I, Y (K, k)	Photosystem II reaction center protein K	polymer	46	5028.1	2	UniProt (Q9F1K9)	Thermosynechococcus vestitus BP-1	PSII-K
10	J, Z (L, l)	Photosystem II reaction center protein L	polymer	37	4299.0	2	UniProt (Q8DIN8)	Thermosynechococcus vestitus BP-1	PSII-L
11	AA, K (M, m)	Photosystem II reaction center protein M	polymer	36	4009.7	2	UniProt (Q8DHA7)	Thermosynechococcus vestitus BP-1	PSII-M
12	BA, L (T, t)	Photosystem II reaction center protein T	polymer	32	3906.7	2	UniProt (Q8DIQ0)	Thermosynechococcus vestitus BP-1	PSII-T,PSII-Tc
13	CA, M (U, u)	Photosystem II extrinsic protein U	polymer	134	15031.0	2	UniProt (Q9F1L5)	Thermosynechococcus vestitus BP-1	PSII-U,PsbU,Photosystem II 12 kDa extrinsic protein,PS II complex 12 kDa extrinsic protein
14	DA, N (V, v)	Photosystem II extrinsic protein V	polymer	163	18046.9	2	UniProt (P0A386)	Thermosynechococcus vestitus BP-1	PsbV,Cytochrome c-549,Cytochrome c-550,Cytochrome c550,Low-potential cytochrome c
15	EA, O (X, x)	Photosystem II reaction center protein X	polymer	41	4322.2	2	UniProt (Q9F1R6)	Thermosynechococcus vestitus BP-1
16	FA, P (Y, y)	Photosystem II reaction center protein Psb30	polymer	46	5039.1	2	UniProt (Q8DJI1)	Thermosynechococcus vestitus BP-1	Photosystem II reaction center protein Ycf12
17	GA, JA (E, e)	Cytochrome b559 subunit alpha	polymer	84	9580.8	2	UniProt (Q8DIP0)	Thermosynechococcus vestitus BP-1	PSII reaction center subunit V
18	HA, KA (O, o)	Photosystem II extrinsic protein O	polymer	272	29637.4	2	UniProt (P0A431)	Thermosynechococcus vestitus BP-1	PsbO,Photosystem II manganese-stabilizing polypeptide,MSP
19	IA, LA (Z, z)	Photosystem II reaction center protein Z	polymer	62	6766.2	2	UniProt (Q8DHJ2)	Thermosynechococcus vestitus BP-1	PSII-Z
20	MA, ZD (A, a)	CA-MN4-O5 CLUSTER	non-polymer		339.8	2	Chemie (OEX)
21	AE, NA (a, A)	FE (II) ION	non-polymer		55.8	2	Chemie (FE2) PubChem (27284)
22	BE, CE, OA, PA (a, A)	CHLORIDE ION	non-polymer		35.5	4	Chemie (CL) PubChem (312)
23	AB, AC, AF, BB, BC... (B, C, b, a, d...)	CHLOROPHYLL A	non-polymer		893.5	70	Chemie (CLA)
24	DG, FE, RC, SA (d, a, D, A)	PHEOPHYTIN A	non-polymer		871.2	4	Chemie (PHO)
25	AH, CF, DF, EF, FH... (k, b, t, a, d...)	BETA-CAROTENE	non-polymer		536.9	20	Chemie (BCR) PubChem (5280489) PubChem (86765360) PubChem (173398668)
26	BG, CD, CG, FF, IE... (c, D, b, a, d...)	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	10	Chemie (LMG) PubChem (446441)
27	JE, KG, WA, YC (a, d, A, D)	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-polymer		749.2	4	Chemie (PL9)
28	DH, FD, IF, KE, RG... (t, D, c, a, d...)	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	non-polymer		795.1	8	Chemie (SQD) PubChem (25147486)
29	DD, ED, FG, GH, HF... (D, d, t, b, x...)	UNKNOWN LIGAND	non-polymer			22	Chemie (UNL)
30	CH, EH, GF, MD, QD... (m, t, b, J, M...)	DODECYL-BETA-D-MALTOSIDE	non-polymer		510.6	10	Chemie (LMT) PubChem (114880)
31	AG, ID, MC, NC, OC... (c, H, C, h)	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	8	Chemie (DGD) PubChem (15991538)
32	GG, UC (d, D)	BICARBONATE ION	non-polymer		61.0	2	Chemie (BCT) PubChem (769)
33	AD, BD, BH, KH, LG... (D, l, E, d, e...)	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	10	Chemie (LHG)
34	GD, SG (F, f)	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	2	Chemie (HEM)
35	HD, TG (H, h)	(3R)-beta,beta-caroten-3-ol	non-polymer		552.9	2	Chemie (RRX) PubChem (5281235)
36	LD, XG (J, j)	MAGNESIUM ION	non-polymer		24.3	2	Chemie (MG) PubChem (888)
37	HH, WD (v, V)	HEME C	non-polymer		618.5	2	Chemie (HEC)
38	MH, PH (O, o)	CALCIUM ION	non-polymer		40.1	2	Chemie (CA) PubChem (271)
39	AI, AJ, BI, BJ, CI... (M, o, T, z, U...)	water	water		18.0	2565	Chemie (HOH)

Sequence modifications

A, a: 1 - 360 (UniProt: Q8DIV4)

PDB	External Database	Details
Thr 185	Val 185	conflict

Contents of the asymmetric unit

Polymers	Number of chains	38
	Total formula weight	625505.1
Non-Polymers*	Number of molecules	186
	Total formula weight	118685.7
All*	Total formula weight	744190.8

*Water molecules are not included.