8IX1: Protonated LHCII nanodisc at low pH value

Cryo-EM structure of protonated LHCII nanodisc at low pH value. Determined by electron microscopy at 2.63 Å resolution. Released 6 Sept 2023.

Method: Electron microscopy
Resolution: 2.63 Å
Organism: Spinacia oleracea
Chains: 3
Atoms: 7,896
Mol. weight: 117.46 kDa
Ligands: CHL, LHG, NEX, XAT
Released: 6 Sept 2023

Explore 8IX1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8IX1 contains 25 α-helices and 2 β-strands across 3 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 G: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	26-28	3
α-helix	55-87	33
α-helix	97-99	3
α-helix	100-105	6
α-helix	112-114	3
α-helix	125-144	20
α-helix	170-201	32
α-helix	205-214	10
α-helix	223-228	6

Chain N: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	55-87	33
α-helix	100-104	5
β-strand	110-111	2	1
α-helix	112-114	3
β-strand	120-121	2	1
α-helix	125-144	20
α-helix	170-201	32
α-helix	205-214	10
α-helix	223-228	6

Chain Y: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	26-28	3
α-helix	55-86	32
α-helix	100-105	6
α-helix	112-114	3
α-helix	125-144	20
α-helix	170-201	32
α-helix	205-214	10
α-helix	223-228	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chlorophyll a-b binding protein, chloroplastic	G, N, Y	protein	218	Spinacia oleracea	P12333 (AlphaFold model)

Sequence of entity 1 (G, N, Y), FASTA

>8IX1_1 Chlorophyll a-b binding protein, chloroplastic (chains G, N, Y)
SPWYGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAM
LGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQVI
LMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVKEIKNGRLAMFSMFG
FFVQAIVTGKGPLENLADHLADPVNNNAWNFATNFVPG

Ligands and cofactors

ID	Name	Formula	Copies
CHL	Chlorophyll B	C55 H70 Mg N4 O6	18
LHG	1,2-dipalmitoyl-phosphatidyl-glycerole	C38 H75 O10 P	3
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	3
XAT	(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-…	C40 H56 O4	3
LUT	(3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol	C40 H56 O2	6
CLA	Chlorophyll a	C55 H72 Mg N4 O5	24

Primary citation

Cryo-EM structures of LHCII in photo-active and photo-protecting states reveal allosteric regulation of light harvesting and excess energy dissipation. Ruan, M., Li, H., Zhang, Y. et al. Nat Plants (2023) 9:1547-1557. DOI 10.1038/s41477-023-01500-2 · PubMed

Other PDB entries of the same protein (UniProt P12333 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8Y15 2.17 Å, Cryo-EM structure of Light-harvesting complex from Spinacia oleracea
8YEE 2.37 Å, Cryo-EM structure of in vitro reconstituted Light-harvesting complex II trimer
8IWZ 2.52 Å, Cryo-EM structure of unprotonated LHCII in detergent solution at low pH value
8IWX 2.59 Å, Cryo-EM structure of unprotonated LHCII in detergent solution at high pH value
4LCZ 2.6 Å, Crystal structure of a multilayer-packed major light-harvesting complex
8IX0 2.64 Å, Cryo-EM structure of unprotonated LHCII nanodisc at high pH value
8IWY 2.68 Å, Cryo-EM structure of protonated LHCII in detergent solution at low pH value
1RWT 2.72 Å, Crystal Structure of Spinach Major Light-harvesting complex at 2.72 Angstrom Resolution
8IX2 2.8 Å, Cryo-EM structure of unprotonated LHCII nanodisc at low pH value
3JCU 3.2 Å, Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angstrom resolution
8Z9D 3.22 Å, cryo-EM structure of PSII-LHCII megacomplex from spinach

Browse structure collections

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