7D1U

Cryo-EM Structure of PSII at 2.08 angstrom resolution

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, U (A, a)	Photosystem II protein D1	polymer	334	37029.2	2	UniProt (P51765) Pfam (PF00124)	Thermosynechococcus vulcanus	PSII D1 protein,Photosystem II Q(B) protein
2	B, V (B, b)	Photosystem II CP47 reaction center protein	polymer	505	56068.7	2	UniProt (D0VWR1) Pfam (PF00421)	Thermosynechococcus vulcanus	PSII 47 kDa protein,Protein CP-47
3	C, W (C, c)	Photosystem II CP43 reaction center protein	polymer	451	49207.3	2	UniProt (D0VWR7) Pfam (PF00421)	Thermosynechococcus vulcanus	PSII 43 kDa protein,Protein CP-43
4	D, X (D, d)	Photosystem II D2 protein	polymer	342	38419.9	2	UniProt (D0VWR8) Pfam (PF00124)	Thermosynechococcus vulcanus	PSII D2 protein,Photosystem Q(A) protein
5	E, Y (E, e)	Cytochrome b559 subunit alpha	polymer	81	9321.5	2	UniProt (P12238) Pfam (PF00283) Pfam (PF00284)	Thermosynechococcus vulcanus	PSII reaction center subunit V
6	F, Z (F, f)	Cytochrome b559 subunit beta	polymer	34	3868.6	2	UniProt (P12239) Pfam (PF00283)	Thermosynechococcus vulcanus	PSII reaction center subunit VI
7	AA, G (H, h)	Photosystem II reaction center protein H	polymer	63	7057.3	2	UniProt (P19052) Pfam (PF00737)	Thermosynechococcus vulcanus	PSII-H
8	BA, H (I, i)	Photosystem II reaction center protein I	polymer	36	4196.0	2	UniProt (P12240) Pfam (PF02532)	Thermosynechococcus vulcanus	PSII-I,PSII 4.4 kDa protein
9	CA, I (J, j)	Photosystem II reaction center protein J	polymer	37	3756.4	2	UniProt (Q7DGD4) Pfam (PF01788)	Thermosynechococcus vulcanus	PSII-J
10	DA, J (K, k)	Photosystem II reaction center protein K	polymer	37	4101.9	2	UniProt (P19054) Pfam (PF02533)	Thermosynechococcus vulcanus	PSII-K
11	EA, K (L, l)	Photosystem II reaction center protein L	polymer	37	4299.0	2	UniProt (P12241) Pfam (PF02419)	Thermosynechococcus vulcanus	PSII-L
12	FA, L (M, m)	Photosystem II reaction center protein M	polymer	34	3835.5	2	UniProt (P12312) Pfam (PF05151)	Thermosynechococcus vulcanus	PSII-M
13	GA, M (O, o)	Photosystem II manganese-stabilizing polypeptide	polymer	244	26651.7	2	UniProt (D0VWR2) Pfam (PF01716)	Thermosynechococcus vulcanus	MSP,Extrinsic protein O of oxygen-evolving complex
14	HA, N (T, t)	Photosystem II reaction center protein T	polymer	31	3777.6	2	UniProt (P12313) Pfam (PF01405)	Thermosynechococcus vulcanus	PSII-Tc
15	IA, O (U, u)	Photosystem II 12 kDa extrinsic protein	polymer	97	10966.3	2	UniProt (P56152) Pfam (PF06514)	Thermosynechococcus vulcanus	PS II complex 12 kDa extrinsic protein,PSII-U,Extrinsic protein U of oxygen-evolving complex
16	JA, P (V, v)	Cytochrome c-550	polymer	137	15148.3	2	UniProt (P0A387) Pfam (PF14495)	Thermosynechococcus vulcanus	Cytochrome c550,Low-potential cytochrome c,Extrinsic protein V of oxygen-evolving complex
17	KA, Q (Y, y)	Photosystem II reaction center protein Ycf12	polymer	30	3228.0	2	UniProt (D0VWR3) Pfam (PF05969)	Thermosynechococcus vulcanus
18	LA, R (X, x)	Photosystem II reaction center protein X	polymer	40	4191.0	2	UniProt (D0VWR4) Pfam (PF06596)	Thermosynechococcus vulcanus
19	MA, S (Z, z)	Photosystem II reaction center protein Z	polymer	62	6766.2	2	UniProt (D0VWR5) Pfam (PF01737)	Thermosynechococcus vulcanus	PSII-Z
20	NA, T (R, r)	Photosystem II protein Y	polymer	34	3859.7	2	UniProt (P0DM37) Pfam (PF06298)	Thermosynechococcus vulcanus
21	JE, OA (a, A)	CA-MN4-O5 CLUSTER	non-polymer		339.8	2	Chemie (OEX)
22	KE, PA (a, A)	FE (II) ION	non-polymer		55.8	2	Chemie (FE2)
23	LE, ME, QA, RA (a, A)	CHLORIDE ION	non-polymer		35.5	4	Chemie (CL)
24	AF, AG, BD, BF, BG... (b, c, D, B, C...)	CHLOROPHYLL A	non-polymer		893.5	70	Chemie (CLA)
25	CD, PE, UA, WG (D, a, A, d)	PHEOPHYTIN A	non-polymer		871.2	4	Chemie (PHO)
26	CC, CE, FD, GE, MG... (B, T, D, Y, c...)	BETA-CAROTENE	non-polymer		536.9	20	Chemie (BCR)
27	BH, HD, SE, TH, UE... (d, D, a, 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)
28	AH, GD, TE, YA (d, D, a, 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)
29	AB, AD, AI, BC, BE... (A, C, x, B, M...)	UNKNOWN LIGAND	non-polymer			36	Chemie (UNL)
30	BB, WE (A, a)	BICARBONATE ION	non-polymer		61.0	2	Chemie (BCT)
31	EC, FH, LD, RG, SF... (C, d, D, c, b...)	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	10	Chemie (LMG)
32	AC, CH, DH, EH, HH... (B, d, e, D, E...)	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	10	Chemie (LHG)
33	LH, OG, PG, QG, RD... (h, c, H, C)	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	8	Chemie (DGD)
34	JH, PD (e, E)	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	2	Chemie (HEM)
35	KH, QD (h, H)	(3R)-beta,beta-caroten-3-ol	non-polymer		552.9	2	Chemie (RRX)
36	AE, BI, IE, NH, QH... (M, z, Z, i, j...)	DODECYL-BETA-D-MALTOSIDE	non-polymer		510.6	8	Chemie (LMT)
37	PH, VD (j, J)	MAGNESIUM ION	non-polymer		24.3	2	Chemie (MG)
38	FE, YH (V, v)	HEME C	non-polymer		618.5	2	Chemie (HEC)
39	AJ, BJ, CI, CJ, DI... (i, j, A, k, B...)	water	water		18.0	2121	Chemie (HOH)

Sequence modifications

A, a: 11 - 344 (UniProt: P51765)

PDB	External Database	Details
Pro 279	Arg 279	conflict

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

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

M, m: 1 - 34 (UniProt: P12312)

PDB	External Database	Details
Leu 8	Phe 8	conflict

Contents of the asymmetric unit

Polymers	Number of chains	40
	Total formula weight	591500.7
Non-Polymers*	Number of molecules	196
	Total formula weight	117584.3
All*	Total formula weight	709085.1

*Water molecules are not included.