1RWT: Spinach Major Light-harvesting complex

Crystal Structure of Spinach Major Light-harvesting complex at 2.72 Angstrom Resolution. Determined by X-ray diffraction at 2.72 Å resolution. Released 30 Mar 2004.

Method: X-ray diffraction
Resolution: 2.72 Å
Organism: Spinacia oleracea
Chains: 10
Atoms: 29,039
Mol. weight: 419.14 kDa
Ligands: CHL, DGD, LHG, NEX
Released: 30 Mar 2004

Explore 1RWT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1RWT contains 105 α-helices and 40 β-strands across 10 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, D and J: 11 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	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

Chain B: 10 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	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
α-helix	221-224	4

Chain C: 10 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	97-105	9
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
α-helix	221-224	4

Chains E and H: 10 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	101-105	5
β-strand	110	1	9
α-helix	112-114	3
β-strand	121	1	9
α-helix	124-144	21
β-strand	146	1	10
β-strand	149	1	10
α-helix	159-161	3
α-helix	170-201	32
α-helix	205-214	10
α-helix	221-224	4

Chains F and G: 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	11
α-helix	112-114	3
β-strand	121	1	11
α-helix	124-144	21
β-strand	146	1	12
β-strand	149	1	12
α-helix	159-161	3
α-helix	170-201	32
α-helix	205-214	10
α-helix	221-224	4

Chain I: 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	97-105	9
β-strand	110	1	17
α-helix	112-114	3
β-strand	121	1	17
α-helix	124-144	21
β-strand	146	1	18
β-strand	149	1	18
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, chloroplast	A, B, C, D, E, F, G, H, I, J	protein	232	Spinacia oleracea	P12333 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA

>1RWT_1 Chlorophyll A-B binding protein, chloroplast (chains A, B, C, D, E, F, G, H, I, J)
RKTAGKPKTVQSSSPWYGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFAK
NRELEVIHCRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVH
AQSILAIWACQVILMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVKE
IKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWNFATNFVPGK

Ligands and cofactors

ID	Name	Formula	Copies
CHL	Chlorophyll B	C55 H70 Mg N4 O6	60
DGD	Digalactosyl diacyl glycerol (DGDG)	C51 H96 O15	10
LHG	1,2-dipalmitoyl-phosphatidyl-glycerole	C38 H75 O10 P	10
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	10
XAT	(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-…	C40 H56 O4	10
LUT	(3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol	C40 H56 O2	20
BNG	nonyl beta-D-glucopyranoside	C15 H30 O6	10
CLA	Chlorophyll a	C55 H72 Mg N4 O5	80

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

Primary citation

Crystal structure of spinach major light-harvesting complex at 2.72 A resolution. Liu, Z., Yan, H., Wang, K. et al. Nature (2004) 428:287-292. DOI 10.1038/nature02373 · 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
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
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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1RWT is part of these collections:

Photosynthesis

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