8C29

Cryo-EM structure of photosystem II C2S2 supercomplex from Norway spruce (Picea abies) at 2.8 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, X (A, a)	Photosystem II protein D1	polymer	353	38803.2	2	UniProt (P50155) Pfam (PF00124)	Picea abies (Norway spruce)	PSII D1 protein,Photosystem II Q(B) protein
2	B, Y (B, b)	Photosystem II CP47 reaction center protein	polymer	508	56375.5	2	UniProt (R4ZGX1) Pfam (PF00421)	Picea abies (Norway spruce)
3	C, Z (C, c)	Photosystem II CP43 reaction center protein	polymer	473	51785.3	2	UniProt (R4ZGZ0) Pfam (PF00421)	Picea abies (Norway spruce)
4	AA, D (D, d)	Photosystem II D2 protein	polymer	353	39483.1	2	UniProt (R4ZGX6) Pfam (PF00124)	Picea abies (Norway spruce)	PSII D2 protein,Photosystem Q(A) protein
5	BA, E (E, e)	Cytochrome b559 subunit alpha	polymer	83	9478.6	2	UniProt (R4ZGW6) Pfam (PF00283) Pfam (PF00284)	Picea abies (Norway spruce)	PSII reaction center subunit V
6	CA, F (F, f)	Cytochrome b559 subunit beta	polymer	39	4476.3	2	UniProt (R4ZGT7) Pfam (PF00283)	Picea abies (Norway spruce)	PSII reaction center subunit VI
7	DA, G, JA, M, SA... (G, N, Y, g, n...)	Chlorophyll a-b binding protein, chloroplastic	polymer	275	29112.0	6	UniProt (Q40771) Pfam (PF00504)	Picea abies (Norway spruce)
8	EA, H (H, h)	Photosystem II reaction center protein H	polymer	75	7941.1	2	UniProt (R4ZGS7) Pfam (PF00737)	Picea abies (Norway spruce)	PSII-H
9	FA, I (I, i)	Photosystem II reaction center protein I	polymer	36	4185.0	2	UniProt (R4ZGS4) Pfam (PF02532)	Picea abies (Norway spruce)	PSII-I,PSII 4.8 kDa protein
10	GA, J (K, k)	Photosystem II reaction center protein K	polymer	59	6804.1	2	UniProt (R4ZGX8) Pfam (PF02533)	Picea abies (Norway spruce)
11	HA, K (L, l)	Photosystem II reaction center protein L	polymer	38	4475.2	2	UniProt (R4ZGV2) Pfam (PF02419)	Picea abies (Norway spruce)	PSII-L
12	IA, L (M, m)	Photosystem II reaction center protein M	polymer	37	3952.6	2	UniProt (A2CHR7) Pfam (PF05151)	Picea abies (Norway spruce)
13	KA, N (O, o)	Oxygen-evolving enhancer protein 1, chloroplastic	polymer	341	36089.5	2	UniProt (A9NRV4) Pfam (PF01716)	Picea abies (Norway spruce)
14	LA, O (R, r)	Chlorophyll a-b binding protein, chloroplastic	polymer	300	32767.9	2	UniProt (A9NKX0) Pfam (PF00504)	Picea abies (Norway spruce)
15	MA, P (S, s)	Chlorophyll a-b binding protein, chloroplastic	polymer	303	32287.9	2	UniProt (A9NKM0) Pfam (PF00504)	Picea abies (Norway spruce)
16	NA, Q (T, t)	Photosystem II reaction center protein T	polymer	35	3962.8	2	UniProt (R4ZGU2) Pfam (PF01405)	Picea abies (Norway spruce)	PSII-T
17	OA, R (U, u)	Photosystem II 5 kDa protein, chloroplastic	polymer	133	14189.5	2	UniProt (A9NJW3)	Picea abies (Norway spruce)
18	PA, S (V, v)	Photosystem II reaction center protein Ycf12	polymer	33	3490.3	2	UniProt (R4ZGY5) Pfam (PF05969)	Picea abies (Norway spruce)
19	QA, T (W, w)	PSII 6.1 kDa protein	polymer	146	15266.5	2	UniProt (A9NLC2) Pfam (PF07123)	Picea abies (Norway spruce)
20	RA, U (X, x)	Photosystem II PsbX	polymer	129	12956.9	2	UniProt (A9NTS2) Pfam (PF06596)	Picea abies (Norway spruce)
21	TA, W (Z, z)	Photosystem II reaction center protein Z	polymer	62	6412.6	2	UniProt (R4ZGT1) Pfam (PF01737)	Picea abies (Norway spruce)
22	UA, VH (A, a)	FE (II) ION	non-polymer		55.8	2	Chemie (FE2)
23	AI, AM, AN, AO, BL... (a, n, s, y, g...)	CHLOROPHYLL A	non-polymer		893.5	154	Chemie (CLA)
24	HK, ID, YA, ZH (d, D, A, a)	PHEOPHYTIN A	non-polymer		871.2	4	Chemie (PHO)
25	AB, AC, BI, LL, NE... (A, B, a, h, H...)	BETA-CAROTENE	non-polymer		536.9	20	Chemie (BCR)
26	BB, CI, RE, UE (A, a, L, M)	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	non-polymer		795.1	4	Chemie (SQD)
27	AJ, BC, CB, EG, FK... (b, B, A, R, c...)	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	12	Chemie (LMG)
28	AH, DB, DI, FD, IK... (X, A, a, C, d...)	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE	non-polymer		705.0	12	Chemie (3PH)
29	EB, EI, MK, ND (A, a, d, 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)
30	DG, FB, FI, GM, HJ... (R, A, a, n, b...)	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	18	Chemie (LHG)
31	AD, AK, BD, BK, CD... (C, c, b, B, A...)	ALPHA-LINOLENIC ACID	non-polymer		278.4	26	Chemie (LNL)
32	BJ, CC (b, B)	PALMITOLEIC ACID	non-polymer		254.4	2	Chemie (PAM)
33	OE, QK, WC, XJ (H, d, C, c)	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	4	Chemie (DGD)
34	XC, YJ (C, c)	MAGNESIUM ION	non-polymer		24.3	2	Chemie (MG)
35	ED, VN (C, y)	(2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL	non-polymer		430.7	2	Chemie (VIV)
36	GK, HD (d, D)	BICARBONATE ION	non-polymer		61.0	2	Chemie (BCT)
37	GJ, QD (b, D)	DIACYL GLYCEROL	non-polymer		625.0	2	Chemie (DGA)
38	RK, SD (f, F)	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	2	Chemie (HEM)
39	AE, AF, AL, BE, BF... (G, N, g, y, Y...)	CHLOROPHYLL B	non-polymer		907.5	50	Chemie (CHL)
40	AG, CM, DM, GL, HE... (R, n, g, G, N...)	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL	non-polymer		568.9	18	Chemie (LUT)
41	BG, FG, FM, IL, JE... (R, n, g, G, N...)	(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	10	Chemie (NEX)
42	BH, CG, EM, HM, LE... (Y, R, n, G, N...)	(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	8	Chemie (XAT)
43	AP, BP, CP, DP, EP... (T, U, V, Y, Z...)	water	water		18.0	280	Chemie (HOH)

Sequence modifications

A, a: 1 - 353 (UniProt: P50155)

PDB	External Database	Details
Phe 295	Leu 295	conflict

B, b: 1 - 508 (UniProt: R4ZGX1)

PDB	External Database	Details
Phe 464	Ser 464	conflict

C, c: 1 - 473 (UniProt: R4ZGZ0)

PDB	External Database	Details
Leu 175	Pro 175	conflict
Leu 433	Pro 433	conflict

D, d: 1 - 353 (UniProt: R4ZGX6)

PDB	External Database	Details
Leu 280	Ser 280	conflict
Phe 312	Ser 312	conflict

G, N, Y, g, n, y: 1 - 275 (UniProt: Q40771)

PDB	External Database	Details
Ile 224	Leu 224	conflict
Leu 249	Ile 249	conflict
Asn 261	Thr 261	conflict

K, k: 1 - 59 (UniProt: R4ZGX8)

PDB	External Database	Details
Phe 31	Ser 31	conflict
Phe 45	Ser 45	conflict

M, m: 1 - 37 (UniProt: A2CHR7)

PDB	External Database	Details
Leu 25	Pro 25	conflict

R, r: 1 - 300 (UniProt: A9NKX0)

PDB	External Database	Details
Thr 54	Pro 54	conflict
Ala 56	-	insertion
Val 57	-	insertion
Ala 58	-	insertion
Lys 59	-	insertion
Pro 60	-	insertion
Lys 61	-	insertion
Thr 62	-	insertion
Lys 63	-	insertion
Ala 64	-	insertion
Val 65	-	insertion
Ala 66	-	insertion
Lys 67	-	insertion

S, s: 1 - 303 (UniProt: A9NKM0)

PDB	External Database	Details
Leu 213	Ala 213	conflict

W, w: 1 - 146 (UniProt: A9NLC2)

PDB	External Database	Details
Met 98	Leu 98	conflict

X, x: 1 - 129 (UniProt: A9NTS2)

PDB	External Database	Details
Ala 80	Val 80	conflict

Z, z: 1 - 62 (UniProt: R4ZGT1)

PDB	External Database	Details
Leu 17	Phe 17	conflict

Contents of the asymmetric unit

Polymers	Number of chains	46
	Total formula weight	945039.4
Non-Polymers*	Number of molecules	358
	Total formula weight	270517.1
All*	Total formula weight	1215556.4

*Water molecules are not included.