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) | 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) PubChem (573) PubChem (21672398) PubChem (176490061) PubChem (177696266) PubChem (46783370) PubChem (46846294) PubChem (54603957) PubChem (54612003) PubChem (86765360) PubChem (5315709) PubChem (5280489) PubChem (91827292) PubChem (92863345) PubChem (5353436) PubChem (5356616) PubChem (5927371) PubChem (124919640) PubChem (92863346) PubChem (92863347) PubChem (92863348) PubChem (6477957) PubChem (100990628) PubChem (101525094) PubChem (101525095) PubChem (9828626) PubChem (10256668) PubChem (12305639) PubChem (12305640) PubChem (12305642) PubChem (12305644) PubChem (12305647) PubChem (12305652) PubChem (146673260) PubChem (152743364) PubChem (124919639) PubChem (160505766) PubChem (129651951) PubChem (132274419) PubChem (145925599) PubChem (159562859) PubChem (172654026) PubChem (172878405) PubChem (173398668) | |||
| 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) PubChem (25147486) PubChem (25235342) PubChem (42607399) PubChem (159321) PubChem (481096) PubChem (5459390) PubChem (102201395) PubChem (134765349) PubChem (9810997) PubChem (9918745) PubChem (10219110) PubChem (10373133) PubChem (14463145) | |||
| 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) PubChem (24865462) PubChem (24865463) PubChem (50904896) PubChem (53480668) PubChem (46936671) PubChem (448441) PubChem (447899) PubChem (4629344) PubChem (15991538) PubChem (154573294) PubChem (171123158) PubChem (134746152) PubChem (140529801) | |||
| 29 | DB, UG (A, a) | FE (II) ION | non-polymer | 55.8 | 2 | Chemie (FE2) PubChem (27284) | |||
| 30 | AC, BE, CC, CE, CL... (B, L, r, w, s...) | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE | non-polymer | 723.0 | 26 | Chemie (LHG) PubChem (46936292) PubChem (446440) PubChem (73416066) PubChem (65144) PubChem (9547104) PubChem (13305396) PubChem (11846227) PubChem (138986743) | |||
| 31 | NI, XC (d, D) | BICARBONATE ION | non-polymer | 61.0 | 2 | Chemie (BCT) PubChem (769) | |||
| 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) PubChem (23304240) PubChem (20286) PubChem (21881166) PubChem (5375177) PubChem (6323474) PubChem (6325820) PubChem (6433402) | |||
| 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) PubChem (24728610) PubChem (177565809) PubChem (25202165) PubChem (177696530) PubChem (44481270) PubChem (46835684) PubChem (25245095) PubChem (53477744) PubChem (53477774) PubChem (181579) PubChem (441664) PubChem (53477760) PubChem (57922343) PubChem (31380) PubChem (90820720) PubChem (448437) PubChem (89305995) PubChem (91240120) PubChem (91519940) PubChem (91007743) PubChem (91330154) PubChem (91467158) PubChem (5281243) PubChem (93535598) PubChem (94424894) PubChem (100935514) PubChem (101351907) PubChem (101351906) PubChem (5368396) PubChem (6325550) PubChem (6433159) PubChem (93971688) PubChem (93971689) PubChem (93971690) PubChem (93971691) PubChem (94424892) PubChem (94424893) PubChem (131801656) PubChem (101351905) PubChem (101351908) PubChem (101351909) PubChem (101351910) PubChem (101727094) PubChem (102093134) PubChem (102514741) PubChem (12085680) PubChem (10210008) PubChem (10257404) PubChem (139335388) PubChem (12359017) PubChem (16061195) PubChem (16061196) PubChem (16061204) PubChem (162679657) PubChem (162945700) PubChem (162945708) PubChem (125183271) PubChem (125183272) PubChem (125183273) PubChem (125183613) PubChem (125183614) PubChem (126970006) PubChem (175679236) PubChem (175679086) PubChem (131801655) PubChem (139595700) PubChem (152743345) PubChem (156583347) PubChem (159139983) PubChem (162945701) PubChem (162945702) PubChem (162945703) PubChem (162945704) PubChem (162945705) PubChem (162945706) PubChem (162945707) PubChem (162945709) PubChem (169423521) PubChem (169954357) PubChem (172748694) | |||
| 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) PubChem (177697037) PubChem (21158515) PubChem (52948899) PubChem (4481261) PubChem (5282217) PubChem (159749) PubChem (5320120) PubChem (5281247) PubChem (101866355) PubChem (6384259) PubChem (101052392) PubChem (101866356) PubChem (101866357) PubChem (102060371) PubChem (10908146) PubChem (12358959) PubChem (162910894) PubChem (162910891) PubChem (162910895) PubChem (139033583) PubChem (162910892) PubChem (162910893) PubChem (162910896) PubChem (169502056) PubChem (172012198) | |||
| 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) PubChem (24970201) PubChem (46936684) PubChem (53477762) PubChem (179930) PubChem (51346155) PubChem (448438) PubChem (92096) PubChem (5282218) PubChem (5315242) PubChem (98049827) PubChem (101341889) PubChem (101341891) PubChem (6852159) PubChem (126456015) PubChem (6384269) PubChem (6442428) PubChem (98049828) PubChem (101341888) PubChem (101341890) PubChem (101341892) PubChem (101341893) PubChem (101341894) PubChem (101341895) PubChem (9851662) PubChem (12358664) PubChem (12358665) PubChem (12358669) PubChem (155293357) PubChem (162964874) PubChem (163187351) PubChem (125183415) PubChem (125183416) PubChem (125183417) PubChem (177696491) PubChem (129888894) PubChem (137331554) PubChem (152743429) PubChem (162964869) PubChem (162964870) PubChem (162964871) PubChem (162964872) PubChem (162964873) PubChem (162964875) PubChem (162964876) PubChem (163186889) PubChem (169544055) PubChem (171036315) PubChem (172817291) |
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 |
Sequence viewer
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 |
