8GN1

Crystal structure of DBBQ-bound photosystem II complex

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, T (A, a)	Photosystem II protein D1	polymer	344	38235.6	2	UniProt (P51765) Pfam (PF00124)	Thermostichus vulcanus	PSII D1 protein,Photosystem II Q(B) protein
2	B, U (B, b)	Photosystem II CP47 reaction center protein	polymer	505	56068.7	2	UniProt (D0VWR1) Pfam (PF00421)	Thermostichus vulcanus	PSII 47 kDa protein,Protein CP-47
3	C, V (C, c)	Photosystem II CP43 reaction center protein	polymer	455	49668.8	2	UniProt (D0VWR7) Pfam (PF00421)	Thermostichus vulcanus	PSII 43 kDa protein,Protein CP-43
4	D, W (D, d)	Photosystem II D2 protein	polymer	342	38419.9	2	UniProt (D0VWR8) Pfam (PF00124)	Thermostichus vulcanus	PSII D2 protein,Photosystem Q(A) protein
5	E, X (E, e)	Cytochrome b559 subunit alpha	polymer	83	9449.6	2	UniProt (P12238) Pfam (PF00283) Pfam (PF00284)	Thermostichus vulcanus	PSII reaction center subunit V
6	F, Y (F, f)	Cytochrome b559 subunit beta	polymer	44	4936.7	2	UniProt (P12239) Pfam (PF00283)	Thermostichus vulcanus	PSII reaction center subunit VI
7	G, Z (H, h)	Photosystem II reaction center protein H	polymer	63	7057.3	2	UniProt (P19052) Pfam (PF00737)	Thermostichus vulcanus	PSII-H
8	AA, H (I, i)	Photosystem II reaction center protein I	polymer	38	4438.3	2	UniProt (P12240) Pfam (PF02532)	Thermostichus vulcanus	PSII-I,PSII 4.4 kDa protein
9	BA, I (J, j)	Photosystem II reaction center protein J	polymer	40	4105.9	2	UniProt (Q7DGD4) Pfam (PF01788)	Thermostichus vulcanus	PSII-J
10	CA, J (K, k)	Photosystem II reaction center protein K	polymer	37	4101.9	2	UniProt (P19054) Pfam (PF02533)	Thermostichus vulcanus	PSII-K
11	DA, K (L, l)	Photosystem II reaction center protein L	polymer	37	4299.0	2	UniProt (P12241) Pfam (PF02419)	Thermostichus vulcanus	PSII-L
12	EA, L (M, m)	Photosystem II reaction center protein M	polymer	36	4009.7	2	UniProt (P12312) Pfam (PF05151)	Thermostichus vulcanus	PSII-M
13	FA, M (O, o)	Photosystem II manganese-stabilizing polypeptide	polymer	244	26651.7	2	UniProt (D0VWR2) Pfam (PF01716)	Thermostichus vulcanus	MSP,Extrinsic protein O of oxygen-evolving complex
14	GA, N (T, t)	Photosystem II reaction center protein T	polymer	32	3906.7	2	UniProt (P12313) Pfam (PF01405)	Thermostichus vulcanus	PSII-Tc
15	HA, O (U, u)	Photosystem II 12 kDa extrinsic protein	polymer	104	11656.0	2	UniProt (P56152) Pfam (PF06514)	Thermostichus vulcanus	PS II complex 12 kDa extrinsic protein,PSII-U
16	IA, P (V, v)	Cytochrome c-550	polymer	137	15148.3	2	UniProt (P0A387) Pfam (PF14495)	Thermostichus vulcanus	Cytochrome c550,Low-potential cytochrome c,Extrinsic protein V of oxygen-evolving complex
17	JA, Q (Y, y)	Photosystem II reaction center protein Ycf12	polymer	30	3228.0	2	UniProt (D0VWR3) Pfam (PF05969)	Thermostichus vulcanus
18	KA, R (X, x)	Photosystem II reaction center protein X	polymer	40	4191.0	2	UniProt (D0VWR4) Pfam (PF06596)	Thermostichus vulcanus
19	LA, S (Z, z)	Photosystem II reaction center protein Z	polymer	62	6794.2	2	UniProt (D0VWR5) Pfam (PF01737)	Thermostichus vulcanus	PSII-Z
20	MA (R)	Photosystem II protein Y	polymer	41	4590.6	1	UniProt (Q8DKM3) Pfam (PF06298) UniProt (by SIFTS) (P0DM37)	Thermostichus vulcanus
21	HI, NA (a, A)	CA-MN4-O5 CLUSTER	non-polymer		339.8	2	Chemie (OEX)
22	II, OA (a, A)	FE (II) ION	non-polymer		55.8	2	Chemie (FE2)
23	JI, KI, PA, QA (a, A)	CHLORIDE ION	non-polymer		35.5	4	Chemie (CL)
24	AC, AL, BC, BF, BL... (B, c, D, b, d...)	CHLOROPHYLL A	non-polymer		893.5	70	Chemie (CLA)
25	OI, PI, TA, UA (a, A)	PHEOPHYTIN A	non-polymer		871.2	4	Chemie (PHO)
26	AE, AI, CO, DF, EC... (C, Y, k, D, B...)	BETA-CAROTENE	non-polymer		536.9	20	Chemie (BCR)
27	AG, FI, HC, LN, PG... (F, a, B, f, L...)	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	non-polymer		795.1	8	Chemie (SQD)
28	EE, IC, JF, KE, NL... (C, B, D, c, i...)	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	10	Chemie (LMG)
29	AB, CI, GB, GG, GI... (A, Z, I, a, m...)	DODECYL-BETA-D-MALTOSIDE	non-polymer		510.6	20	Chemie (LMT)
30	BB, BI, BO, CB, CK... (A, X, k, b, m...)	UNKNOWN LIGAND	non-polymer		258.1	44	Chemie (UNL)
31	DB, EF, PM, PP (A, D, d, x)	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)
32	EB, FB, VI, WI (A, a)	2,5-bis(bromanyl)cyclohexa-2,5-diene-1,4-dione	non-polymer		265.9	4	Chemie (K2I)
33	HB, LI (A, a)	BICARBONATE ION	non-polymer		61.0	2	Chemie (BCT)
34	AD, AH, AJ, AM, AN... (B, O, a, c, d...)	DIMETHYL SULFOXIDE	non-polymer		78.1	128	Chemie (DMS)
35	EJ, JO, NB, SG, UK (b, o, B, O, c)	CALCIUM ION	non-polymer		40.1	5	Chemie (CA)
36	AK, BK, CJ, DJ, FE... (b, C, I, B, D...)	heptyl 1-thio-beta-D-glucopyranoside	non-polymer		294.4	21	Chemie (HTG)
37	AF, AO, CP, DI, DP... (D, k, v, Z, a...)	GLYCEROL	non-polymer		92.1	21	Chemie (GOL)
38	BE, CE, DE, EG, FF... (C, H, D, c, h)	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	9	Chemie (DGD)
39	EO, GF, GN, HF, IF... (l, D, e, L, d...)	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	10	Chemie (LHG)
40	BG, IN (F, e)	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	2	Chemie (HEM)
41	DG, NN (H, h)	(3R)-beta,beta-caroten-3-ol	non-polymer		552.9	2	Chemie (RRX)
42	KG, YN (J, j)	MAGNESIUM ION	non-polymer		24.3	2	Chemie (MG)
43	BP, PH (v, V)	HEME C	non-polymer		618.5	2	Chemie (HEC)
44	AQ, AR, BQ, BR, CQ... (I, u, J, v, K...)	water	water		18.0	2573	Chemie (HOH)

Sequence modifications

A, a: 1 - 344 (UniProt: P51765)

PDB	External Database	Details
Pro 279	Arg 279	conflict

C, c: 23 - 473 (UniProt: D0VWR7)

PDB	External Database	Details
Asn 19	-	expression tag
Ser 20	-	expression tag
Ile 21	-	expression tag
Phe 22	-	expression tag

K, k: 10 - 46 (UniProt: P19054)

PDB	External Database	Details
Leu 33	Phe 24	conflict
Trp 39	Val 30	conflict

M, m: 1 - 36 (UniProt: P12312)

PDB	External Database	Details
Leu 8	Phe 8	conflict

Contents of the asymmetric unit

Polymers	Number of chains	39
	Total formula weight	597325.6
Non-Polymers*	Number of molecules	396
	Total formula weight	155399.8
All*	Total formula weight	752725.4

*Water molecules are not included.