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) PubChem (27284) | |||
| 31 | BP, CP, HDA, IDA, KD... (a, Aa, A, AA) | CHLORIDE ION | non-polymer | 35.5 | 8 | Chemie (CL) PubChem (312) | |||
| 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) 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) | |||
| 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) PubChem (23304240) PubChem (20286) PubChem (21881166) PubChem (5375177) PubChem (6323474) PubChem (6325820) PubChem (6433402) | |||
| 36 | AH, AL, AM, AS, AT... (11, D, K, g, n...) | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE | non-polymer | 723.0 | 55 | Chemie (LHG) PubChem (46936292) PubChem (446440) PubChem (73416066) PubChem (65144) PubChem (9547104) PubChem (13305396) PubChem (11846227) PubChem (138986743) | |||
| 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) 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) | |||
| 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) 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) | |||
| 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) 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) | |||
| 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) 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) | |||
| 43 | DBA, GAA, ON, WJ (RR, KK, R, C) | DODECYL-ALPHA-D-MALTOSIDE | non-polymer | 510.6 | 4 | Chemie (LMU) PubChem (16220143) PubChem (24802120) PubChem (25021193) PubChem (44119948) PubChem (114880) PubChem (46936627) PubChem (53393702) PubChem (56845466) PubChem (58112562) PubChem (58253045) PubChem (60087035) PubChem (68322761) PubChem (68338004) PubChem (68441652) PubChem (445456) PubChem (70796428) PubChem (70813879) PubChem (70839937) PubChem (75487624) PubChem (59615220) PubChem (3481630) PubChem (2802066) PubChem (89796216) PubChem (91094859) PubChem (90817611) PubChem (91608950) PubChem (95566087) PubChem (102565427) PubChem (95566088) PubChem (95566089) PubChem (95566090) PubChem (96327540) PubChem (97038234) PubChem (97038235) PubChem (97294875) PubChem (98046621) PubChem (98046622) PubChem (98046623) PubChem (100976848) PubChem (101111379) PubChem (101111381) PubChem (102219025) PubChem (117716045) PubChem (117753833) PubChem (118443377) PubChem (9849225) PubChem (123281924) PubChem (10413991) PubChem (124184997) PubChem (124196217) PubChem (124196220) PubChem (140505128) PubChem (153835411) PubChem (155885597) PubChem (126735853) PubChem (126735860) PubChem (169619620) PubChem (173767704) PubChem (173885518) PubChem (129720403) PubChem (134694723) PubChem (140479759) PubChem (140841257) PubChem (154810097) PubChem (159812235) PubChem (163184859) | |||
| 44 | AR, BX, CL, CX, DS... (c, BB, D, h, Aa...) | DIGALACTOSYL DIACYL GLYCEROL (DGDG) | non-polymer | 949.3 | 20 | 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) | |||
| 45 | CW, LP, SDA, UK (AA, a, Aa, D) | BICARBONATE ION | non-polymer | 61.0 | 4 | Chemie (BCT) PubChem (769) | |||
| 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 |
Sequence viewer
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 |
