3JCU: Spinach PSII-LHCII supercomplex

Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angstrom resolution. Determined by electron microscopy at 3.2 Å resolution. Released 25 May 2016.

Method
Electron microscopy
Resolution
3.2 Å
Organism
Spinacia oleracea
Chains
50
Atoms
75,994
Mol. weight
1276.9 kDa
Ligands
OEX, FE2, CLA, PHO
Released
25 May 2016

Explore 3JCU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3JCU contains 388 α-helices and 236 β-strands across 50 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains a and A: 21 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix13-219
α-helix32-5423
α-helix55-573
β-strand58192
β-strand67192
α-helix71-733
β-strand81-82293
α-helix83-864
α-helix102-1076
α-helix110-13627
α-helix143-15513
α-helix156-1605
α-helix161-1655
α-helix168-1703
α-helix172-1732
β-strand174-175293
α-helix176-19015
α-helix192-1943
α-helix196-22025
β-strand223194
β-strand224195
α-helix233-2364
β-strand243196
β-strand246194
α-helix248-25811
α-helix268-29326
β-strand297197
β-strand307198
α-helix3121
β-strand313198
α-helix3141
β-strand315145
α-helix317-33115
Chains b and B: 24 helices, 27 β-strands
ElementResiduesLengthSheet
β-strand3-429
α-helix5-1410
α-helix16-4429
α-helix62-676
β-strand73110
β-strand79110
α-helix93-11624
β-strand120111
β-strand124112
β-strand131112
α-helix135-15218
α-helix153-1586
β-strand167-168213
β-strand177-178213
α-helix187-1904
α-helix196-21823
α-helix220-2212
β-strand222114
α-helix223-2286
α-helix234-25825
α-helix265-2684
α-helix272-2765
α-helix279-29214
α-helix298-3047
α-helix307-3126
β-strand314115
α-helix315-3173
α-helix330-3334
β-strand336-340516
β-strand343117
β-strand346-347218
β-strand353-354218
β-strand355-356219
α-helix358-3603
β-strand370-371219
β-strand377119
β-strand380120
β-strand384121
α-helix385-3873
β-strand391120
α-helix392-3954
β-strand398118
β-strand400122
β-strand402117
β-strand410122
α-helix414-42411
β-strand427115
β-strand430-433416
α-helix447-47428
α-helix476-4805
β-strand482195
Chains c and C: 23 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix28-314
α-helix35-428
α-helix46-7429
α-helix88-947
β-strand99137
α-helix101-1033
β-strand105137
α-helix109-13022
α-helix131-1355
α-helix154-18027
β-strand185-187338
β-strand195-197338
α-helix206-2138
α-helix223-2264
α-helix230-25324
α-helix255-2573
α-helix258-2636
α-helix268-29225
α-helix299-3024
α-helix306-32318
β-strand342-343239
β-strand349-350239
α-helix354-3585
α-helix367-3693
β-strand370-371239
β-strand374-375239
α-helix377-3804
α-helix386-39712
β-strand402197
α-helix422-45332
β-strand459140
α-helix465-4684
α-helix470-4712
Chains d and D: 19 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix14-229
α-helix31-5323
β-strand57145
β-strand63145
β-strand78146
α-helix79-824
α-helix83-853
α-helix101-1066
α-helix109-13527
α-helix142-15312
α-helix154-1596
α-helix160-1634
α-helix167-1693
α-helix171-1722
β-strand173146
α-helix175-18915
α-helix195-22026
β-strand222147
β-strand223140
β-strand241196
β-strand244147
α-helix246-25510
α-helix264-28926
α-helix299-3079
α-helix314-33320
α-helix335-3373
α-helix343-3453
Chains e and E: 6 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix10-156
α-helix17-3923
α-helix42-476
α-helix49-513
α-helix52-554
β-strand57150
β-strand60150
α-helix72-8110
Chains f and F: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix18-4124
Chains g and G: 11 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix26-283
α-helix32-332
α-helix55-8733
α-helix101-1055
β-strand110152
α-helix112-1143
β-strand121152
α-helix124-14421
α-helix159-1613
α-helix166-1683
α-helix170-20132
α-helix205-21410
α-helix221-2277
Chains h and H: 2 helices, 2 β-strands
ElementResiduesLengthSheet
β-strand15111
α-helix18-2811
β-strand34114
α-helix40-6122

17 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Photosystem II protein D1A, aprotein344Spinacia oleraceaP69560 (AlphaFold model)
Photosystem II CP47 reaction center proteinB, bprotein508Spinacia oleraceaP04160 (AlphaFold model)
Photosystem II CP43 reaction center proteinC, cprotein473Spinacia oleraceaP06003 (AlphaFold model)
Photosystem II D2 proteinD, dprotein353Spinacia oleraceaP06005 (AlphaFold model)
Cytochrome b559 subunit alphaE, eprotein83Spinacia oleraceaP69383
Cytochrome b559 subunit betaF, fprotein39Spinacia oleraceaP60128
Chlorophyll a-b binding protein, chloroplasticG, N, Y, g, n, yprotein267Spinacia oleraceaP12333
Photosystem II reaction center protein HH, hprotein73Spinacia oleraceaP05146
Protein Photosystem II reaction center protein II, iprotein36Spinacia oleraceaP62103
Photosystem II reaction center protein JJ, jprotein40Spinacia oleraceaQ9M3L2
Photosystem II reaction center protein KK, kprotein59Spinacia oleraceaP12163
Protein Photosystem II reaction center protein LL, lprotein38Spinacia oleraceaP60139

11 more molecules are not listed.

Sequence of entity 1 (A, a), FASTA
>3JCU_1 Photosystem II protein D1 (chains A, a)
MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDI
DGIREPVSGSLLYGNNIISGAIIPTSAAIGLHFYPIWEAASVDEWLYNGGPYELIVLHFL
LGVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTF
NFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANEGYRFG
QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGIWFTALGISTMAFNLNGF
NFNQSVVDSQGRVINTWADIINRANLGMEVMHERNAHNFPLDLA
Sequence of entity 2 (B, b), FASTA
>3JCU_2 Photosystem II CP47 reaction center protein (chains B, b)
MGLPWYRVHTVVLNDPGRLISVHIMHTALVAGWAGSMALYELAVFDPSDPVLDPMWRQGM
FVIPFMTRLGITNSWGGWSITGGTITDPGIWSYEGVAGAHIMFSGLCFLAAIWHWVYWDL
EIFSDERTGKPSLDLPKIFGIHLFLSGVACFGFGAFHVTGLYGPGIWVSDPYGLTGKVQP
VSPAWGVEGFDPFVPGGIASHHIAAGTLGILAGLFHLSVRPPQRLYKGLRMGNIETVLSS
SIAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDQGYFQQEIYRRVSAGLAENQSFSE
AWSKIPEKLAFYDYIGNNPAKGGLFRAGSMDNGDGIAVGWLGHPIFRDKEGRELFVRRMP
TFFETFPVVLIDGDGIVRADVPFRRAESKYSVEQVGVTVEFYGGELNGVSYSDPATVKKY
ARRAQLGEIFELDRATLKSDGVFRSSPRGWFTFGHASFALLFFFGHIWHGSRTLFRDVFA
GIDPDLDVQVEFGAFQKIGDPTTRRQGV
Sequence of entity 3 (C, c), FASTA
>3JCU_3 Photosystem II CP43 reaction center protein (chains C, c)
MKTLYSLRRFYPVETLFNGTLTLAGRDQETTGFAWWAGNARLINLSGKLLGAHVAHAGLI
VFWAGAMNLFEVAHFVPEKPMYEQGLILLPHLATLGWGVGPGGEVIDTFPYFVSGVLHLI
SSAVLGFGGIYHALLGPETLEESFPFFGYVWKDRNKMTTILGIHLILLGIGAFLLVFKAL
YFGGVYDTWAPGGGDVRKITNVTLSPSIIFGCLLKSPFGGEGWIVSVDDLEDIIGGHVWI
GVICILGGIWHILTKPFAWARRALVWSGEAYLSYSLAALSVFGFIACCFVWFNNTAYPSE
FYGPTGPEASQAQAFTFLVRDQRLGANVGSAQGPTGLGKYLMRSPTGEVIFGGETMRFWD
LRAPWLEPLRGPNGLDLSRLKKDIQPWQERRSAEYMTHAPLGSLNSVGGVATEINAVNYV
SPRSWLSTSHFVLGFFLFVGHLWHAGRARAAAAGFEKGIDRDFEPVLSMTPLN
Sequence of entity 4 (D, d), FASTA
>3JCU_4 Photosystem II D2 protein (chains D, d)
MTIAVGKFTKDEKDLFDSMDDWLRRDRFVFVGWSGLLLFPCAYFALGGWFTGTTFVTSWY
THGLASSYLEGCNFLTAAVSTPANSLAHSLLLLWGPEAQGDFTRWCQLGGLWAFVALHGA
FALIGFMLRQFELARSVQLRPYNAIAFSGPIAVFVSVFLIYPLGQSGWFFAPSFGVAAIF
RFILFFQGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTLFEDGDGANTFRAFNPTQ
AEETYSMVTANRFWSQIFGVAFSNKRWLHFFMLFVPVTGLWMSALGVVGLALNLRAYDFV
SQEIRAAEDPEFETFYTKNILLNEGIRAWMAAQDQPHENLIFPEEVLPRGNAL
Sequence of entity 5 (E, e), FASTA
>3JCU_5 Cytochrome b559 subunit alpha (chains E, e)
MSGSTGERSFADIITSIRYWVIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNEYFTESR
QGIPLITGRFDSLEQLDEFSRSF
Sequence of entity 6 (F, f), FASTA
>3JCU_6 Cytochrome b559 subunit beta (chains F, f)
MTIDRTYPIFTVRWLAIHGLAVPTVFFLGSISAMQFIQR
Sequence of entity 7 (G, N, Y, g, n, y), FASTA
>3JCU_7 Chlorophyll a-b binding protein, chloroplastic (chains G, N, Y, g, n, y)
MASSTMALSSPSLAGKAVKLGPTASEIIGEGRITMRKTAGKPKTVQSSSPWYGPDRVKYL
GPFSGESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAMLGALGCVFPELL
ARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQVILMGAVEGYRIAG
GPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGP
LENLADHLADPVNNNAWNFATNFVPGK
Sequence of entity 8 (H, h), FASTA
>3JCU_8 Photosystem II reaction center protein H (chains H, h)
MATQTVESSSRSRPKPTTVGALLKPLNSEYGKVAPGWGTTPLMGVAMALFAVFLSIILEI
YNSSVLLDGISMN
Sequence of entity 9 (I, i), FASTA
>3JCU_9 Protein  Photosystem II reaction center protein I (chains I, i)
MLTLKLFVYTVVIFFVSLFIFGFLSNDPGRNPGREE
Sequence of entity 10 (J, j), FASTA
>3JCU_10 Photosystem II reaction center protein J (chains J, j)
MADTTGRIPLWIIGTVAGILVIGLVGIFFYGSYSGLGSSL
Sequence of entity 11 (K, k), FASTA
>3JCU_11 Photosystem II reaction center protein K (chains K, k)
MLNIFSLICLNSALYSSSFFFGKLPEAYAFLSPIVDFMPVIPLFFFLLAFVWQAAVSFR
Sequence of entity 12 (L, l), FASTA
>3JCU_12 Protein Photosystem II reaction center protein L (chains L, l)
MTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN

Ligands and cofactors

IDNameFormulaCopies
OEXCa-MN4-O5 clusterCa Mn4 O52
FE2FE (II) ionFe2
CLAChlorophyll aC55 H72 Mg N4 O5156
PHOPheophytin aC55 H74 N4 O54
BCRBeta-caroteneC40 H5620
SQD1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerolC41 H78 O12 S6
LMG1,2-distearoyl-monogalactosyl-diglycerideC45 H86 O1010
DGDDigalactosyl diacyl glycerol (DGDG)C51 H96 O158
BCTBicarbonate ionC H O32
PL92,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-he…C53 H80 O22
LHG1,2-dipalmitoyl-phosphatidyl-glyceroleC38 H75 O10 P18
HEMProtoporphyrin IX containing FEC34 H32 Fe N4 O42
CHLChlorophyll BC55 H70 Mg N4 O650
LUT(3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diolC40 H56 O218
XAT(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-…C40 H56 O48
NEX(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimeth…C40 H56 O410

Water and common crystallization additives (CL) are not listed.

Primary citation

Structure of spinach photosystem II-LHCII supercomplex at 3.2 A resolution. Wei, X.P., Su, X.D., Cao, P. et al. Nature (2016) 534:69-74. DOI 10.1038/nature18020

Other PDB entries of the same protein (UniProt P69560 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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