4LCZ: Multilayer-packed major light-harvesting complex

Crystal structure of a multilayer-packed major light-harvesting complex. Determined by X-ray diffraction at 2.6 Å resolution. Released 7 May 2014.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Spinacia oleracea
Chains: 3
Atoms: 8,016
Mol. weight: 118.4 kDa
Ligands: LHG, CHL, CLA, CAC
Released: 7 May 2014

Explore 4LCZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LCZ contains 28 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.

Chain A: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-33	3
α-helix	55-86	32
α-helix	100-105	6
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

Chain B: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	26-29	4
α-helix	32-33	2
α-helix	55-87	33
α-helix	100-105	6
β-strand	110	1	3
α-helix	112-114	3
β-strand	121	1	3
α-helix	124-144	21
β-strand	146	1	4
β-strand	149	1	4
α-helix	159-161	3
α-helix	170-201	32
α-helix	205-214	10

Chain C: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	26-29	4
α-helix	32-33	2
α-helix	55-86	32
α-helix	97-100	4
α-helix	101-105	5
β-strand	110	1	5
α-helix	112-114	3
β-strand	121	1	5
α-helix	124-144	21
β-strand	146	1	6
β-strand	149	1	6
α-helix	159-161	3
α-helix	170-201	32
α-helix	205-214	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Major chlorophyll a/b binding protein LHCb1.3	A, B, C	protein	224	Spinacia oleracea	P12333 (AlphaFold model)

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

>4LCZ_1 Major chlorophyll a/b binding protein LHCb1.3 (chains A, B, C)
TVQSSSPWYGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIH
CRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIW
ACQVILMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVKEIKNGRLAM
FSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWNFATNFVPGK

Ligands and cofactors

ID	Name	Formula	Copies
LHG	1,2-dipalmitoyl-phosphatidyl-glycerole	C38 H75 O10 P	3
CHL	Chlorophyll B	C55 H70 Mg N4 O6	18
CLA	Chlorophyll a	C55 H72 Mg N4 O5	24
CAC	Cacodylate ion	C2 H6 As O2	3
ZN	Zinc ion	Zn	5
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
LUT	(3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol	C40 H56 O2	6

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

Primary citation

Crystal structure of a multilayer packed major light-harvesting complex: implications for grana stacking in higher plants. Wan, T., Li, M., Zhao, X. et al. Mol Plant (2014) 7:916-919. DOI 10.1093/mp/ssu005 · 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
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

Browse structure collections

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