8Z9D

cryo-EM structure of PSII-LHCII megacomplex from spinach

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, UB, UC, WA (A, a, AA, Aa)	Photosystem II protein D1	polymer	351	38804.2	4	UniProt (P69560) Pfam (PF00124)	Spinacia oleracea (spinach)	PSII D1 protein,32 kDa thylakoid membrane protein,Photosystem II Q(B) protein
2	B, JC, KB, LA (Oo, O, o, OO)	Oxygen-evolving enhancer protein 1, chloroplastic	polymer	332	35207.4	4	UniProt (P12359) Pfam (PF01716)	Spinacia oleracea (spinach)	OEE1,33 kDa subunit of oxygen evolving system of photosystem II,33 kDa thylakoid membrane protein,OEC 33 kDa subunit
3	C, LB, MC, OA (Rr, R, r, RR)	Chlorophyll a-b binding protein, chloroplastic	polymer	286	31046.3	4	UniProt (A0A9R0HRF2) Pfam (PF00504)	Spinacia oleracea (spinach)
4	D, MB, NC, PA (Ss, S, s, SS)	Chlorophyll a-b binding protein, chloroplastic	polymer	295	31341.8	4	UniProt (A0A9R0IJF3) Pfam (PF00504)	Spinacia oleracea (spinach)
5	E, NB, OC, QA (Tt, T, t, TT)	Photosystem II reaction center protein T	polymer	33	3825.6	4	UniProt (P61840) Pfam (PF01405)	Spinacia oleracea (spinach)	PSII-T
6	F, OB, PC, RA (Uu, U, u, UU)	Photosystem II 5 kDa protein, chloroplastic	polymer	99	10676.6	4	UniProt (A0A9R0J8H2)	Spinacia oleracea (spinach)
7	G, PB, QC, SA (Ww, W, w, WW)	Photosystem II reaction center W protein, chloroplastic	polymer	137	14186.1	4	UniProt (Q41387) Pfam (PF07123)	Spinacia oleracea (spinach)	PSII 6.1 kDa protein
8	H, QB, RC, TA (Xx, X, x, XX)	Photosystem II reaction center X protein, chloroplastic	polymer	117	11958.1	4	UniProt (A0A9R0JQ89) Pfam (PF06596)	Spinacia oleracea (spinach)
9	AD, BC, CB, DA, HD... (Yy, G, N, Y, g...)	Chlorophyll a-b binding protein, chloroplastic	polymer	267	28433.4	12	UniProt (A0A9R0JBE4) Pfam (PF00504) UniProt (by SIFTS) (P12333)	Spinacia oleracea (spinach)
10	J, SB, TC, VA (Zz, Z, z, ZZ)	Photosystem II reaction center protein Z	polymer	62	6541.7	4	UniProt (Q9M3M6) Pfam (PF01737)	Spinacia oleracea (spinach)	PSII-Z
11	K, TB (44, 4)	Chlorophyll a-b binding protein CP24, chloroplastic	polymer	259	27693.5	2	UniProt (P36494) Pfam (PF00504)	Spinacia oleracea (spinach)
12	KC, L, MA, N (Pp, p, P, PP)	Oxygen-evolving enhancer protein 2, chloroplastic	polymer	267	28495.9	4	UniProt (P12302) Pfam (PF01789)	Spinacia oleracea (spinach)	OEE2,23 kDa subunit of oxygen evolving system of photosystem II,23 kDa thylakoid membrane protein,OEC 23 kDa subunit
13	LC, M, NA, O (Qq, q, Q, QQ)	Oxygen-evolving enhancer protein 3, chloroplastic	polymer	232	24884.4	4	UniProt (P12301) Pfam (PF05757)	Spinacia oleracea (spinach)	OEE3,16 kDa subunit of oxygen evolving system of photosystem II,OEC 16 kDa subunit
14	P, Q, S, T (11, 22, 1, 2)	Chlorophyll a-b binding protein, chloroplastic	polymer	267	28429.2	4	UniProt (A4F3R4) Pfam (PF00504) UniProt (by SIFTS) (P12333)	Spinacia oleracea (spinach)
15	R, U (33, 3)	Chlorophyll a-b binding protein, chloroplastic	polymer	264	28512.4	2	UniProt (A0A9R0J656) Pfam (PF00504)	Spinacia oleracea (spinach)
16	V, X (0, 00)	Photosystem II 10 kDa polypeptide, chloroplastic	polymer	140	14409.4	2	UniProt (P10690) Pfam (PF04725)	Spinacia oleracea (spinach)
17	W, Y (5, 55)	Photosystem II reaction center proteins PsbY, chloroplastic	polymer	199	20678.2	2	UniProt (P80470) Pfam (PF06298)	Spinacia oleracea (spinach)	L-arginine-metabolizing enzyme,L-AME
18	WB, WC, YA, Z (C, c, CC, Cc)	Photosystem II CP43 reaction center protein	polymer	473	51880.6	4	UniProt (P06003) Pfam (PF00421)	Spinacia oleracea (spinach)	PSII 43 kDa protein,Photosystem II 44 kDa chlorophyll apoprotein,Protein CP-43
19	AA, XB, XC, ZA (D, d, DD, Dd)	Photosystem II D2 protein	polymer	352	39422.0	4	UniProt (P06005) Pfam (PF00124)	Spinacia oleracea (spinach)	PSII D2 protein,Photosystem Q(A) protein
20	AB, BA, YC, ZB (E, e, EE, Ee)	Cytochrome b559 subunit alpha	polymer	83	9393.5	4	UniProt (P69383) Pfam (PF00283) Pfam (PF00284)	Spinacia oleracea (spinach)	PSII reaction center subunit V
21	AC, BB, CA, ZC (F, f, FF, Ff)	Cytochrome b559 subunit beta	polymer	39	4502.4	4	UniProt (P60128) Pfam (PF00283)	Spinacia oleracea (spinach)	PSII reaction center subunit VI
22	BD, CC, DB, EA (H, h, HH, Hh)	Photosystem II reaction center protein H	polymer	73	7735.0	4	UniProt (P05146) Pfam (PF00737)	Spinacia oleracea (spinach)	PSII-H,Photosystem II 10 kDa phosphoprotein
23	CD, DC, EB, FA (I, i, II, Ii)	Photosystem II reaction center protein I	polymer	36	4170.9	4	UniProt (P62103) Pfam (PF02532)	Spinacia oleracea (spinach)	PSII-I,PSII 4.8 kDa protein
24	DD, EC, FB, GA (J, j, JJ, Jj)	Photosystem II reaction center protein J	polymer	40	4117.8	4	UniProt (Q9M3L2) Pfam (PF01788)	Spinacia oleracea (spinach)	PSII-J
25	ED, FC, GB, HA (K, k, KK, Kk)	Photosystem II reaction center protein K	polymer	59	6751.0	4	UniProt (P12163) Pfam (PF02533)	Spinacia oleracea (spinach)	PSII-K
26	FD, GC, HB, IA (L, l, LL, Ll)	Photosystem II reaction center protein L	polymer	38	4498.1	4	UniProt (P60150) Pfam (PF02419)	Spinacia oleracea (spinach)	PSII-L
27	GD, HC, IB, JA (M, m, MM, Mm)	Photosystem II reaction center protein M	polymer	34	3783.5	4	UniProt (P62112) Pfam (PF05151)	Spinacia oleracea (spinach)	PSII-M
28	VB, VC, XA, YB (b, BB, B, Bb)	Photosystem II CP47 reaction center protein	polymer	508	56207.9	4	UniProt (P04160) Pfam (PF00421)	Spinacia oleracea (spinach)	PSII 47 kDa protein,Protein CP-47
29	ID, PEA, QV, ZO (A, Cc, AA, a)	CA-MN4-O5 CLUSTER	non-polymer		339.8	4	Chemie (OEX)
30	AP, GDA, JD, RV (a, Aa, A, AA)	FE (II) ION	non-polymer		55.8	4	Chemie (FE2)
31	BP, CP, HDA, IDA, KD... (a, Aa, A, AA)	CHLORIDE ION	non-polymer		35.5	8	Chemie (CL)
32	ADA, AE, AEA, AF, AFA... (YY, Rr, Bb, Ss, Cc...)	CHLOROPHYLL A	non-polymer		893.5	374	Chemie (CLA)
33	CY, GP, HP, MDA, NDA... (DD, a, Aa, A, D...)	PHEOPHYTIN A	non-polymer		871.2	8	Chemie (PHO)
34	BM, CS, DFA, DO, EFA... (K, h, Cc, T, b...)	BETA-CAROTENE	non-polymer		536.9	44	Chemie (BCR)
35	FR, GY, LFA, RD, YK... (d, DD, Dd, 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	6	Chemie (PL9)
36	AH, AL, AM, AS, AT... (11, D, K, g, n...)	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	55	Chemie (LHG)
37	AZ, BW, CM, DM, EX... (B, AA, L, CC, l...)	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	non-polymer		795.1	14	Chemie (SQD)
38	BR, EL, EO, ES, EW... (c, F, W, j, AA...)	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	22	Chemie (LMG)
39	ACA, AGA, AHA, BCA, BE... (SS, Gg, Nn, Rr, 44...)	CHLOROPHYLL B	non-polymer		907.5	140	Chemie (CHL)
40	BDA, BF, CDA, CF, CO... (YY, Ss, S, s, 2...)	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL	non-polymer		568.9	38	Chemie (LUT)
41	AAA, ABA, BS, CAA, HU... (GG, NN, g, y, 44...)	(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL	non-polymer		600.9	18	Chemie (XAT)
42	BBA, DDA, IGA, ME, NN... (NN, YY, Gg, Rr, R...)	(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL	non-polymer		600.9	14	Chemie (NEX)
43	DBA, GAA, ON, WJ (RR, KK, R, C)	DODECYL-ALPHA-D-MALTOSIDE	non-polymer		510.6	4	Chemie (LMU)
44	AR, BX, CL, CX, DS... (c, BB, D, h, Aa...)	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	20	Chemie (DGD)
45	CW, LP, SDA, UK (AA, a, Aa, D)	BICARBONATE ION	non-polymer		61.0	4	Chemie (BCT)
46	DL, IR, JZ, QFA (E, e, EE, Ee)	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	4	Chemie (HEM)

Sequence modifications

Xx, X, x, XX: 1 - 117 (UniProt: A0A9R0JQ89)

PDB	External Database	Details
Gly 45	Ser 45	conflict

Contents of the asymmetric unit

Polymers	Number of chains	112
	Total formula weight	2355227.9
Non-Polymers*	Number of molecules	781
	Total formula weight	630960.3
All*	Total formula weight	2986188.3

*Water molecules are not included.