9LK4

Cryo-EM structure of Lhcb4.1-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, W (A, a)	Photosystem II protein D1	polymer	353	38961.3	2	UniProt (P83755) Pfam (PF00124)	Arabidopsis thaliana (thale cress)	PSII D1 protein,Photosystem II Q(B) protein
2	B, X (B, b)	Photosystem II CP47 reaction center protein	polymer	508	56091.8	2	UniProt (P56777) Pfam (PF00421)	Arabidopsis thaliana (thale cress)	PSII 47 kDa protein,Protein CP-47
3	C, Y (C, c)	Photosystem II CP43 reaction center protein	polymer	473	51915.5	2	UniProt (P56778) Pfam (PF00421)	Arabidopsis thaliana (thale cress)	PSII 43 kDa protein,Protein CP-43
4	D, Z (D, d)	Photosystem II D2 protein	polymer	353	39575.3	2	UniProt (P56761) Pfam (PF00124)	Arabidopsis thaliana (thale cress)	PSII D2 protein,Photosystem Q(A) protein
5	AA, E (E, e)	Cytochrome b559 subunit alpha	polymer	83	9393.5	2	UniProt (P56779) Pfam (PF00283) Pfam (PF00284)	Arabidopsis thaliana (thale cress)	PSII reaction center subunit V
6	BA, F (F, f)	Cytochrome b559 subunit beta	polymer	39	4428.2	2	UniProt (P62095) Pfam (PF00283)	Arabidopsis thaliana (thale cress)	PSII reaction center subunit VI
7	CA, G, JA, N (G, N, g, n)	Chlorophyll a-b binding protein 2, chloroplastic	polymer	267	28251.0	4	UniProt (P0CJ48) Pfam (PF00504)	Arabidopsis thaliana (thale cress)	Chlorophyll a-b protein 165,CAB-165,LHCII type I CAB-2
8	DA, H (H, h)	Photosystem II reaction center protein H	polymer	73	7706.9	2	UniProt (P56780) Pfam (PF00737)	Arabidopsis thaliana (thale cress)	PSII-H,Photosystem II 10 kDa phosphoprotein
9	EA, I (I, i)	Photosystem II reaction center protein I	polymer	36	4170.9	2	UniProt (P62100) Pfam (PF02532)	Arabidopsis thaliana (thale cress)	PSII-I,PSII 4.8 kDa protein
10	FA, J (J, j)	Photosystem II reaction center protein J	polymer	40	4117.8	2	UniProt (P56781) Pfam (PF01788)	Arabidopsis thaliana (thale cress)	PSII-J
11	GA, K (K, k)	Photosystem II reaction center protein K	polymer	61	6977.4	2	UniProt (P56782) Pfam (PF02533)	Arabidopsis thaliana (thale cress)	PSII-K
12	HA, L (L, l)	Photosystem II reaction center protein L	polymer	38	4471.1	2	UniProt (P60129) Pfam (PF02419)	Arabidopsis thaliana (thale cress)	PSII-L
13	IA, M (M, m)	Photosystem II reaction center protein M	polymer	34	3783.5	2	UniProt (P62109) Pfam (PF05151)	Arabidopsis thaliana (thale cress)	PSII-M
14	KA, O (O, o)	Oxygen-evolving enhancer protein 1-1, chloroplastic	polymer	332	35180.3	2	UniProt (P23321) Pfam (PF01716)	Arabidopsis thaliana (thale cress)	OEE1,33 kDa subunit of oxygen evolving system of photosystem II,33 kDa thylakoid membrane protein,Manganese-stabilizing protein 1,MSP-1,OEC 33 kDa subunit
15	LA, P (R, r)	Chlorophyll a-b binding protein CP29.1, chloroplastic	polymer	300	32227.4	2	UniProt (Q07473) Pfam (PF00504)	Arabidopsis thaliana (thale cress)	LHCB4.1,LHCII protein 4.1
16	MA, Q (T, t)	Photosystem II reaction center protein T	polymer	33	3825.6	2	UniProt (P61839) Pfam (PF01405)	Arabidopsis thaliana (thale cress)	PSII-T
17	NA, R (U, u)	Photosystem II 5 kDa protein, chloroplastic	polymer	103	11042.9	2	UniProt (Q39195)	Arabidopsis thaliana (thale cress)	PSII-T,Nuclear encoded psbT,PsbTn
18	OA, S (W, w)	Photosystem II reaction center W protein, chloroplastic	polymer	133	13685.8	2	UniProt (Q39194) Pfam (PF07123)	Arabidopsis thaliana (thale cress)	PSII 6.1 kDa protein
19	PA, T (X, x)	(thale cress) hypothetical protein	polymer	116	11826.0	2	UniProt (A0A7G2E9B1) Pfam (PF06596)	Arabidopsis thaliana (thale cress)
20	QA, U (Y, y)	Chlorophyll a-b binding protein 2.2, chloroplastic	polymer	265	28644.4	2	UniProt (Q9S7J7) Pfam (PF00504)	Arabidopsis thaliana (thale cress)	Photosystem II light harvesting complex gene 2.2,Protein LIGHT-HARVESTING CHLOROPHYLL B-BINDING 2.2
21	RA, V (Z, z)	Photosystem II reaction center protein Z	polymer	62	6569.8	2	UniProt (P56790) Pfam (PF01737)	Arabidopsis thaliana (thale cress)	PSII-Z
22	SA, TA (S, s)	Chlorophyll a-b binding protein CP26, chloroplastic	polymer	280	30187.6	2	UniProt (Q9XF89) Pfam (PF00504)	Arabidopsis thaliana (thale cress)	LHCB5,LHCIIc,Light-harvesting complex II protein 5
23	AF, AH, AI, BF, BG... (R, b, c, Y, n...)	CHLOROPHYLL A	non-polymer		893.5	156	Chemie (CLA)
24	LI, OG, WA, WC (d, a, A, D)	PHEOPHYTIN A	non-polymer		871.2	4	Chemie (PHO)
25	AE, DD, GI, HI, KG... (K, F, c, Z, b...)	BETA-CAROTENE	non-polymer		536.9	20	Chemie (BCR)
26	CB, DE, EE, MI, TG... (A, L, M, d, a)	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	non-polymer		795.1	6	Chemie (SQD)
27	AB, BC, BD, DC, QH... (A, B, D, C, b...)	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	8	Chemie (LMG)
28	BB, II, SG, TC, UI... (A, c, a, C, d...)	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	6	Chemie (DGD)
29	DB, UG (A, a)	FE (II) ION	non-polymer		55.8	2	Chemie (FE2)
30	AC, BE, CC, CE, CL... (B, L, r, w, s...)	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	26	Chemie (LHG)
31	NI, XC (d, D)	BICARBONATE ION	non-polymer		61.0	2	Chemie (BCT)
32	AD, RI (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	2	Chemie (PL9)
33	CD, VI (E, e)	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	2	Chemie (HEM)
34	AG, AJ, AK, AM, BJ... (Y, g, n, S, R...)	CHLOROPHYLL B	non-polymer		907.5	52	Chemie (CHL)
35	AN, BN, GG, HG, HK... (s, Y, n, S, g...)	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL	non-polymer		568.9	18	Chemie (LUT)
36	BL, CN, IG, JK, LM... (r, s, Y, n, S...)	(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)
37	AL, EL, FE, NF, PJ... (r, y, N, R, g...)	(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)

Sequence modifications

R, r: 1 - 290 (UniProt: Q07473)

PDB	External Database	Details
Gly 291	-	expression tag
Gly 292	-	expression tag
Gly 293	-	expression tag
Gly 294	-	expression tag
His 295	-	expression tag
His 296	-	expression tag
His 297	-	expression tag
His 298	-	expression tag
His 299	-	expression tag
His 300	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	46
	Total formula weight	922569.9
Non-Polymers*	Number of molecules	322
	Total formula weight	260376.5
All*	Total formula weight	1182946.4

*Water molecules are not included.