8Z9D: PSII-LHCII megacomplex from spinach
cryo-EM structure of PSII-LHCII megacomplex from spinach. Determined by electron microscopy at 3.22 Å resolution. Released 13 Nov 2024.
- Method
- Electron microscopy
- Resolution
- 3.22 Å
- Organism
- Spinacia oleracea
- Chains
- 112
- Atoms
- 171,299
- Mol. weight
- 2986.19 kDa
- Ligands
- OEX, FE2, CLA, PHO
- Released
- 13 Nov 2024
Explore 8Z9D in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8Z9D contains 750 α-helices and 386 β-strands across 112 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.
Chain 0: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 88-91 | 4 | |
| α-helix | 111-135 | 25 | |
Chain 00: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 88-91 | 4 | |
| α-helix | 101 | 1 | |
| α-helix | 111-135 | 25 | |
Chain 1: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 65-67 | 3 | |
| α-helix | 90-121 | 32 | |
| α-helix | 122-124 | 3 | |
| α-helix | 132-137 | 6 | |
| α-helix | 160-179 | 20 | |
| α-helix | 205-235 | 31 | |
| α-helix | 240-249 | 10 | |
Chain 11: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 65-67 | 3 | |
| α-helix | 90-121 | 32 | |
| α-helix | 122-124 | 3 | |
| α-helix | 132-137 | 6 | |
| α-helix | 161-179 | 19 | |
| α-helix | 205-220 | 16 | |
| α-helix | 222-234 | 13 | |
| α-helix | 240-249 | 10 | |
Chain 2: 12 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 61-63 | 3 | |
| α-helix | 67-68 | 2 | |
| α-helix | 90-105 | 16 | |
| α-helix | 111-114 | 4 | |
| α-helix | 116-120 | 5 | |
| α-helix | 121-123 | 3 | |
| α-helix | 159-161 | 3 | |
| α-helix | 162-166 | 5 | |
| α-helix | 169-179 | 11 | |
| α-helix | 205-235 | 31 | |
| α-helix | 240-249 | 10 | |
| α-helix | 258-261 | 4 | |
Chain 22: 10 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 61-63 | 3 | |
| α-helix | 67-68 | 2 | |
| α-helix | 90-113 | 24 | |
| α-helix | 115-120 | 6 | |
| α-helix | 160-161 | 2 | |
| α-helix | 162-166 | 5 | |
| α-helix | 168-179 | 12 | |
| β-strand | 181 | 1 | 64 |
| β-strand | 184 | 1 | 64 |
| β-strand | 193 | 1 | 65 |
| β-strand | 196 | 1 | 65 |
| α-helix | 208-235 | 28 | |
| α-helix | 240-249 | 10 | |
| α-helix | 259-261 | 3 | |
Chain 3: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 56-58 | 3 | |
| α-helix | 85-87 | 3 | |
| α-helix | 88-110 | 23 | |
| α-helix | 115-119 | 5 | |
| α-helix | 131-133 | 3 | |
| α-helix | 162-175 | 14 | |
| α-helix | 202-230 | 29 | |
| α-helix | 237-246 | 10 | |
| α-helix | 253-257 | 5 | |
Chain 33: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 56-58 | 3 | |
| α-helix | 85-106 | 22 | |
| α-helix | 111-118 | 8 | |
| α-helix | 131-133 | 3 | |
| α-helix | 163-173 | 11 | |
| α-helix | 202-228 | 27 | |
| α-helix | 237-246 | 10 | |
| α-helix | 253-255 | 3 | |
89 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Photosystem II protein D1 | A, AA, Aa, a | protein | 351 | Spinacia oleracea | P69560 (AlphaFold model) |
| Oxygen-evolving enhancer protein 1, chloroplastic | O, OO, Oo, o | protein | 332 | Spinacia oleracea | P12359 (AlphaFold model) |
| Chlorophyll a-b binding protein, chloroplastic | R, RR, Rr, r | protein | 286 | Spinacia oleracea | A0A9R0HRF2 (AlphaFold model) |
| Chlorophyll a-b binding protein, chloroplastic | S, SS, Ss, s | protein | 295 | Spinacia oleracea | A0A9R0IJF3 (AlphaFold model) |
| Photosystem II reaction center protein T | T, TT, Tt, t | protein | 33 | Spinacia oleracea | P61840 |
| Photosystem II 5 kDa protein, chloroplastic | U, UU, Uu, u | protein | 99 | Spinacia oleracea | A0A9R0J8H2 |
| Photosystem II reaction center W protein, chloroplastic | W, WW, Ww, w | protein | 137 | Spinacia oleracea | Q41387 |
| Photosystem II reaction center X protein, chloroplastic | X, XX, Xx, x | protein | 117 | Spinacia oleracea | A0A9R0JQ89 |
| Chlorophyll a-b binding protein, chloroplastic | G, GG, Gg, N, NN, Nn, Y, YY, Yy, g, n, y | protein | 267 | Spinacia oleracea | P12333 |
| Photosystem II reaction center protein Z | Z, ZZ, Zz, z | protein | 62 | Spinacia oleracea | Q9M3M6 |
| Chlorophyll a-b binding protein CP24, chloroplastic | 4, 44 | protein | 259 | Spinacia oleracea | P36494 |
| Oxygen-evolving enhancer protein 2, chloroplastic | P, PP, Pp, p | protein | 267 | Spinacia oleracea | P12302 |
16 more molecules are not listed.
Sequence of entity 1 (A, AA, Aa, a), FASTA
>8Z9D_1 Photosystem II protein D1 (chains A, AA, Aa, a)
MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDI
DGIREPVSGSLLYGNNIISGAIIPTSAAIGLHFYPIWEAASVDEWLYNGGPYELIVLHFL
LGVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTF
NFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANEGYRFG
QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGIWFTALGISTMAFNLNGF
NFNQSVVDSQGRVINTWADIINRANLGMEVMHERNAHNFPLDLAAIEAPST
Sequence of entity 2 (O, OO, Oo, o), FASTA
>8Z9D_2 Oxygen-evolving enhancer protein 1, chloroplastic (chains O, OO, Oo, o)
MAASLQASTTFLQPTKVASRNTLQLRSTQNVCKAFGVESASSGGRLSLSLQSDLKELANK
CVDATKLAGLALATSALIASGANAEGGKRLTYDEIQSKTYLEVKGTGTANQCPTVEGGVD
SFAFKPGKYTAKKFCLEPTKFAVKAEGISKNSGPDFQNTKLMTRLTYTLDEIEGPFEVSS
DGTVKFEEKDGIDYAAVTVQLPGGERVPFLFTIKQLVASGKPESFSGDFLVPSYRGSSFL
DPKGRGGSTGYDNAVALPAGGRGDEEELQKENNKNVASSKGTITLSVTSSKPETGEVIGV
FQSLQPSDTDLGAKVPKDVKIEGVWYAQLEQQ
Sequence of entity 3 (R, RR, Rr, r), FASTA
>8Z9D_3 Chlorophyll a-b binding protein, chloroplastic (chains R, RR, Rr, r)
MASASASAAATSSFIGTRLTEVPSNSGKVTCRFGFGAKKVAKKAQPKSGFSTDRPLWYPG
AKAPEYLDGSLVGDYGFDPFGLGKPAEYLQYDYDGLDQNLAKNLAGDIIGTRTESADVKS
TSLQPYSEVFGLQRFRECELIHGRWAMLATLGALTVEGLTGITWQDAGKVELIEGSSYLG
QPLPFSMTTLIWIEVLVIGYIEFQRNAELDTEKRLYPGGTFDPLGLASDPEKKPILQLAE
IKHARLAMVGFLGFAVQAAVTGKGPLNNWVTHLSDPLHTTILDRFL
Sequence of entity 4 (S, SS, Ss, s), FASTA
>8Z9D_4 Chlorophyll a-b binding protein, chloroplastic (chains S, SS, Ss, s)
MASVAASTAAACLGKSELLGNSLNLRSATSAPCSTPSVGPCKIVALFNFGKKAATPPAKS
KAKVAVASPADDELAKWYGPDRRIFLPDGLLDRDDIPEYLNGEVPGDYGYDPFGLGKKPE
DFAKYQAFELIHARWAMLGAAGCVIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGK
NIPINLVLAVVAEVVLLGGAEYYRITNGLDFEDKLHPGGPFDPLGLAKDPDQAALLKVKE
IKNGRLAMFSMFAFFIQAYVTGQGPVENLSAHLSDPFGNNLLTVIGGAAERVPTL
Sequence of entity 5 (T, TT, Tt, t), FASTA
>8Z9D_5 Photosystem II reaction center protein T (chains T, TT, Tt, t)
MEALVYTFLLVSTLGIIFFAIFFREPPKISTKK
Sequence of entity 6 (U, UU, Uu, u), FASTA
>8Z9D_6 Photosystem II 5 kDa protein, chloroplastic (chains U, UU, Uu, u)
MASITMTASFLGTTVSKQPPTHHLRRGVVMAKAMPETTTTTKEETSSKRRDLVFAVAAAA
ACSVARIAMAEEPKRGTPEAKKKYAPVCVTMPSARICYK
Sequence of entity 7 (W, WW, Ww, w), FASTA
>8Z9D_7 Photosystem II reaction center W protein, chloroplastic (chains W, WW, Ww, w)
MATITASSSASLVARASLVHNSRVGVSSSPILGLPSMTKRSKVTCSIENKPSTTETTTTT
NKSMGASLLAAAAAATISNPAMALVDERMSTEGTGLPFGLSNNLLGWILFGVFGLIWALY
FVYASGLEEDEESGLSL
Sequence of entity 8 (X, XX, Xx, x), FASTA
>8Z9D_8 Photosystem II reaction center X protein, chloroplastic (chains X, XX, Xx, x)
MASISAVSMATPITTTTTKTTFFSPLPVVKPQRATLMGQKPRAMGLKVQASLKEKAVTGL
TAAALTASMMVPDVAEAAELAPSLKNFLFSIAAGGVVLTAIVGAVVAVSNFDPVKRA
Sequence of entity 9 (G, GG, Gg, N, NN, Nn, Y, YY, Yy, g, n, y), FASTA
>8Z9D_9 Chlorophyll a-b binding protein, chloroplastic (chains G, GG, Gg, N, NN, Nn, Y, YY, Yy, g, n, y)
MASSTMALSSPSLAGKAVKLGPTASEIIGEGRITMRKTAGKPKTVQSSSPWYGPDRVKYL
GPFSGEAPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAMLGALGCVFPELL
ARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQVILMGAVEGYRIAG
GPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGP
LENLADHLADPVNNNAWNFATNFVPGK
Sequence of entity 10 (Z, ZZ, Zz, z), FASTA
>8Z9D_10 Photosystem II reaction center protein Z (chains Z, ZZ, Zz, z)
MTIAFQLAVFALIATSSILLISVPVVFASPDGWSSNKNIVFSGTSLWLGLVFLVGILNSL
IS
Sequence of entity 11 (4, 44), FASTA
>8Z9D_11 Chlorophyll a-b binding protein CP24, chloroplastic (chains 4, 44)
MAAATSATAIVNGFTSPFLSGGKKSSQSLLFVNSKVGAGVSTTSRKLVVVAAAAAPKKSW
IPAVKGGGNFLDPEWLDGSLPGDFGFDPLGLGKDPAFLKWYREAELIHGRWAMLAVLGIF
VGQAWTGIPWFEAGADPGAVAPFSFGTLLGTQLLLMGWVESKRWVDFFDPDSQSVEWATP
WSRTAENFSNSTGEQGYPGGKFFDPLSLAGTISNGVYNPDTDKLERLKLAEIKHARLAML
AMLIFYFEAGQGKTPLGAL
Sequence of entity 12 (P, PP, Pp, p), FASTA
>8Z9D_12 Oxygen-evolving enhancer protein 2, chloroplastic (chains P, PP, Pp, p)
MASTACFLHHHAAISSPAAGRGSAAQRYQAVSIKPNQIVCKAQKQDDNEANVLNSGVSRR
LALTVLIGAAAVGSKVSPADAAYGEAANVFGKPKKNTEFMPYNGDGFKLLVPSKWNPSKE
KEFPGQVLRYEDNFDATSNLSVLVQPTDKKSITDFGSPEDFLSQVDYLLGKQAYFGKTDS
EGGFDSGVVASANVLESSTPVVDGKQYYSITVLTRTADGDEGGKHQVIAATVKDGKLYIC
KAQAGDKRWFKGAKKFVESATSSFSVA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| OEX | Ca-MN4-O5 cluster | Ca Mn4 O5 | 4 |
| FE2 | FE (II) ion | Fe | 4 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 374 |
| PHO | Pheophytin a | C55 H74 N4 O5 | 8 |
| BCR | Beta-carotene | C40 H56 | 44 |
| PL9 | 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-he… | C53 H80 O2 | 6 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 55 |
| SQD | 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol | C41 H78 O12 S | 14 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 22 |
| CHL | Chlorophyll B | C55 H70 Mg N4 O6 | 140 |
| LUT | (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | C40 H56 O2 | 38 |
| XAT | (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-… | C40 H56 O4 | 18 |
| NEX | (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimeth… | C40 H56 O4 | 14 |
| LMU | Dodecyl-alpha-D-maltoside | C24 H46 O11 | 4 |
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 20 |
| BCT | Bicarbonate ion | C H O3 | 4 |
| HEM | Protoporphyrin IX containing FE | C34 H32 Fe N4 O4 | 4 |
Water and common crystallization additives (CL) are not listed.
Primary citation
Architecture and functional regulation of a plant PSII-LHCII megacomplex. Shan, J., Niedzwiedzki, D.M., Tomar, R.S. et al. Sci Adv (2024) 10:eadq9967-eadq9967. DOI 10.1126/sciadv.adq9967 · PubMed
Other PDB entries of the same protein (UniProt P69560 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3JCU 3.2 Å, Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angstrom resolution
Browse structure collections
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