8GN2

Crystal structure of PPBQ-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)	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)	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)	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)	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)	Thermostichus vulcanus	PSII reaction center subunit V
6	F, Y (F, f)	Cytochrome b559 subunit beta	polymer	44	4936.7	2	UniProt (P12239)	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)	Thermostichus vulcanus	PSII-H
8	AA, H (I, i)	Photosystem II reaction center protein I	polymer	38	4438.3	2	UniProt (P12240)	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)	Thermostichus vulcanus	PSII-J
10	CA, J (K, k)	Photosystem II reaction center protein K	polymer	37	4101.9	2	UniProt (P19054)	Thermostichus vulcanus	PSII-K
11	DA, K (L, l)	Photosystem II reaction center protein L	polymer	37	4299.0	2	UniProt (P12241)	Thermostichus vulcanus	PSII-L
12	EA, L (M, m)	Photosystem II reaction center protein M	polymer	36	4009.7	2	UniProt (P12312)	Thermostichus vulcanus	PSII-M
13	FA, M (O, o)	Photosystem II manganese-stabilizing polypeptide	polymer	244	26651.7	2	UniProt (D0VWR2)	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)	Thermostichus vulcanus	PSII-Tc
15	HA, O (U, u)	Photosystem II 12 kDa extrinsic protein	polymer	104	11656.0	2	UniProt (P56152)	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)	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)	Thermostichus vulcanus
18	KA, R (X, x)	Photosystem II reaction center protein X	polymer	40	4191.0	2	UniProt (D0VWR4)	Thermostichus vulcanus
19	LA, S (Z, z)	Photosystem II reaction center protein Z	polymer	62	6794.2	2	UniProt (D0VWR5)	Thermostichus vulcanus	PSII-Z
20	MA (R)	Photosystem II protein Y	polymer	41	4590.6	1	UniProt (Q8DKM3) Pfam (PF06298)	Thermostichus vulcanus
21	NA, ZG (A, a)	CA-MN4-O5 CLUSTER	non-polymer		339.8	2	Chemie (OEX)
22	AH, OA (a, A)	FE (II) ION	non-polymer		55.8	2	Chemie (FE2) PubChem (27284)
23	BH, CH, PA, QA (a, A)	CHLORIDE ION	non-polymer		35.5	4	Chemie (CL) PubChem (312)
24	AC, AI, BI, CI, DI... (B, b, a, C, c...)	CHLOROPHYLL A	non-polymer		893.5	70	Chemie (CLA)
25	HH, ME, UA, UK (a, D, A, d)	PHEOPHYTIN A	non-polymer		871.2	4	Chemie (PHO)
26	BC, CC, DC, FM, GG... (B, k, T, a, D...)	BETA-CAROTENE	non-polymer		536.9	20	Chemie (BCR) PubChem (573) PubChem (21672398) PubChem (176490061) PubChem (177696266) PubChem (46783370) PubChem (46846294) PubChem (54603957) PubChem (54612003) PubChem (5315709) PubChem (5353436) PubChem (5356616) PubChem (5927371) PubChem (86765360) PubChem (6477957) PubChem (9828626) PubChem (91827292) PubChem (10256668) PubChem (92863346) PubChem (92863347) PubChem (92863348) PubChem (12305639) PubChem (12305640) PubChem (12305642) PubChem (12305644) PubChem (12305647) PubChem (12305652) PubChem (5280489) PubChem (92863345) PubChem (100990628) PubChem (101525094) PubChem (101525095) PubChem (124919640) PubChem (124919639) PubChem (129651951) PubChem (132274419) PubChem (146673260) PubChem (152743364) PubChem (160505766) PubChem (145925599) PubChem (159562859) PubChem (172654026) PubChem (172878405) PubChem (173398668)
27	KH, NL, TE, WF, XA... (a, f, D, L, A)	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) PubChem (25235342) PubChem (42607399) PubChem (5459390) PubChem (159321) PubChem (9810997) PubChem (9918745) PubChem (481096) PubChem (10219110) PubChem (10373133) PubChem (14463145) PubChem (102201395) PubChem (134765349)
28	DK, EC, EK, EL, KE... (c, B, d, C, a...)	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	10	Chemie (LMG)
29	AB, FC, FF, FK, IG... (A, B, E, c, T...)	DODECYL-BETA-D-MALTOSIDE	non-polymer		510.6	17	Chemie (LMT)
30	AG, AJ, AN, BB, CB... (M, b, v, A, C...)	GLYCEROL	non-polymer		92.1	48	Chemie (GOL) PubChem (753)
31	AF, BJ, BM, CJ, CM... (D, b, j, A, E...)	UNKNOWN LIGAND	non-polymer		258.1	57	Chemie (UNL)
32	HB, UH (A, a)	2-phenylcyclohexa-2,5-diene-1,4-dione	non-polymer		184.2	2	Chemie (K3C) PubChem (9688)
33	AL, IB, RE, VH (d, A, D, a)	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) PubChem (20286) PubChem (23304240) PubChem (21881166) PubChem (5375177) PubChem (6323474) PubChem (6325820) PubChem (6433402)
34	DH, JB (a, A)	BICARBONATE ION	non-polymer		61.0	2	Chemie (BCT) PubChem (769)
35	BG, JF, KB, KJ, OL... (O, F, B, c, f...)	CALCIUM ION	non-polymer		40.1	7	Chemie (CA) PubChem (271)
36	AE, BE, CG, GC, GK... (C, O, B, c, d...)	heptyl 1-thio-beta-D-glucopyranoside	non-polymer		294.4	21	Chemie (HTG) PubChem (17754029) PubChem (22844385) PubChem (561567) PubChem (656917) PubChem (71317209) PubChem (135074) PubChem (10979306) PubChem (11335391) PubChem (11392262) PubChem (95858610) PubChem (96361182) PubChem (96361183) PubChem (97041763) PubChem (101138253)
37	BL, CF, CL, DL, JM... (d, E, l, e, D...)	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	10	Chemie (LHG) PubChem (446440) PubChem (46936292) PubChem (73416066) PubChem (65144) PubChem (9547104) PubChem (11846227) PubChem (13305396) PubChem (138986743)
38	AD, AM, BD, BF, CD... (B, i, D, C, O...)	DIMETHYL SULFOXIDE	non-polymer		78.1	31	Chemie (DMS) PubChem (679)
39	AK, BK, CK, LF, SE... (c, H, D, h, C)	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	9	Chemie (DGD) PubChem (24865462) PubChem (24865463) PubChem (448441) PubChem (50904896) PubChem (53480668) PubChem (46936671) PubChem (447899) PubChem (4629344) PubChem (15991538) PubChem (134746152) PubChem (154573294) PubChem (140529801) PubChem (171123158)
40	IF, ML (F, f)	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	2	Chemie (HEM)
41	KF, TL (H, h)	(3R)-beta,beta-caroten-3-ol	non-polymer		552.9	2	Chemie (RRX) PubChem (20056910) PubChem (92111) PubChem (177443103) PubChem (182237) PubChem (44554791) PubChem (5316150) PubChem (6384256) PubChem (91496173) PubChem (5281235) PubChem (101088204) PubChem (124934401) PubChem (102330248) PubChem (102330249) PubChem (102330250) PubChem (124934402) PubChem (124934403) PubChem (124934404) PubChem (152743353) PubChem (163007083) PubChem (163007084) PubChem (168433814) PubChem (169423484)
42	DM, RF (j, J)	MAGNESIUM ION	non-polymer		24.3	2	Chemie (MG) PubChem (888)
43	BN, MG (v, V)	HEME C	non-polymer		618.5	2	Chemie (HEC)
44	AO, BO, CO, DO, EO... (V, Y, X, a, b...)	water	water		18.0	3237	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	336
	Total formula weight	151516.1
All*	Total formula weight	748841.8

*Water molecules are not included.