8Y15: Light-harvesting complex from Spinacia oleracea

Cryo-EM structure of Light-harvesting complex from Spinacia oleracea. Determined by electron microscopy at 2.17 Å resolution. Released 20 Nov 2024.

Method: Electron microscopy
Resolution: 2.17 Å
Organism: Spinacia oleracea
Chains: 3
Atoms: 8,181
Mol. weight: 117 kDa
Ligands: XAT, LHG, NEX, A1LXP
Released: 20 Nov 2024

Explore 8Y15 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y15 contains 33 α-helices and 12 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.

Chains A, B and C: 11 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	32-33	2
α-helix	55-86	32
α-helix	97-100	4
α-helix	101-105	5
β-strand	110	1	1
α-helix	112-114	3
β-strand	121	1	1
α-helix	124-144	21
β-strand	146	1	2
β-strand	149	1	2
α-helix	159-161	3
α-helix	170-201	32
α-helix	205-214	10
α-helix	221-224	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chlorophyll a-b binding protein, chloroplastic	A, B, C	protein	216	Spinacia oleracea	P12333 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8Y15_1 Chlorophyll a-b binding protein, chloroplastic (chains A, B, C)
SPWYGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAM
LGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQVI
LMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVKEIKNGRLAMFSMFG
FFVQAIVTGKGPLENLADHLADPVNNNAWNFATNFV

Ligands and cofactors

ID	Name	Formula	Copies
XAT	(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-…	C40 H56 O4	3
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
A1LXP	Lutein	C40 H56 O2	6
CLA	Chlorophyll a	C55 H72 Mg N4 O5	24
CHL	Chlorophyll B	C55 H70 Mg N4 O6	18

Primary citation

Structure-based validation of recombinant light-harvesting complex II. Seki, S., Miyata, T., Norioka, N. et al. PNAS Nexus (2024) 3:pgae405-pgae405. DOI 10.1093/pnasnexus/pgae405 · PubMed

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

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
8IX1 2.63 Å, Cryo-EM structure of protonated LHCII nanodisc at low pH value
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

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