7VY3: Photosynthetic reaction center L subunit

Structure of photosynthetic LH1-rc super-complex of rhodobacter sphaeroides lacking protein-U. Determined by electron microscopy at 2.63 Å resolution. Released 27 Apr 2022.

Method: Electron microscopy
Resolution: 2.63 Å
Organism: Rhodobacter sphaeroides f. sp. denitrificans
Chains: 25
Atoms: 18,831
Mol. weight: 288.91 kDa
Ligands: BCL, BPH, U10, PGV
Released: 27 Apr 2022

Explore 7VY3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VY3 contains 93 α-helices and 41 β-strands across 25 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 1: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	13-37	25

Chain A: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	13-37	25

Chains B, E, G, J, N, R, T and W: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	13-44	32

Chains D, F and K: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	4-9	6
α-helix	13-37	25
α-helix	43-50	8

Chain H: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	13
β-strand	10	1	13
α-helix	12-34	23
β-strand	43	1	1
β-strand	49	1	1
α-helix	50	1
α-helix	57-61	5
β-strand	62-65	4	4
β-strand	72-75	4	4
β-strand	87-89	3	14
β-strand	98-100	3	14
α-helix	104-107	4
α-helix	110-112	3
α-helix	121-122	2
β-strand	123	1	15
β-strand	129	1	15
β-strand	131-133	3	16
β-strand	141-144	4	7
β-strand	152-154	3	16
β-strand	160-170	11	16
β-strand	175-182	8	16
β-strand	188-192	5	16
α-helix	193-195	3
β-strand	197-198	2	16
β-strand	203-204	2	16
α-helix	210-215	6
α-helix	217-219	3
β-strand	221	1	17
β-strand	224	1	17
α-helix	227-243	17

Chain I: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	4-9	6
α-helix	13-37	25
α-helix	39-41	3
α-helix	43-51	9

Chain L: 19 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
α-helix	7-9	3
β-strand	24-26	3	2
β-strand	29-31	3	2
α-helix	33-56	24
β-strand	65-66	2	3
α-helix	67-70	4
α-helix	71-73	3
α-helix	80-84	5
α-helix	85-111	27
α-helix	116-129	14
α-helix	130-134	5
α-helix	135-139	5
α-helix	142-144	3
α-helix	146-147	2
β-strand	148-149	2	3
α-helix	152-162	11
α-helix	167-169	3
α-helix	171-198	28
β-strand	205	1	4
α-helix	206-208	3
α-helix	209-220	12
β-strand	222	1	5
α-helix	226-249	24
β-strand	251	1	6
β-strand	255	1	6
α-helix	261-263	3
α-helix	264-267	4

Chain M: 20 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	7
α-helix	16-17	2
β-strand	29	1	8
β-strand	35	1	9
α-helix	37-40	4
β-strand	46	1	9
β-strand	47	1	5
β-strand	51	1	8
α-helix	54-77	24
α-helix	82-87	6
β-strand	94	1	10
α-helix	95-98	4
α-helix	99-101	3
α-helix	109-111	3
α-helix	113-139	27
α-helix	145-158	14
α-helix	159-163	5
α-helix	164-168	5
α-helix	171-173	3
β-strand	177	1	10
α-helix	181-192	12
α-helix	196-198	3
α-helix	200-225	26
α-helix	227-229	3
α-helix	234-239	6
α-helix	243-256	14
α-helix	265-286	22
β-strand	287	1	11
β-strand	291	1	11
α-helix	294-299	6
β-strand	300	1	12
β-strand	302	1	12

8 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
Photosynthetic reaction center L subunit	L	protein	281	Rhodobacter sphaeroides f. sp. denitrificans	P0C0Y8 (AlphaFold model)
Reaction center protein M chain	M	protein	307	Rhodobacter sphaeroides f. sp. denitrificans	P0C0Y9 (AlphaFold model)
Photosynthetic reaction center subunit H	H	protein	260	Rhodobacter sphaeroides f. sp. denitrificans	P0C0Y7 (AlphaFold model)
Antenna pigment protein alpha chain	1, A, D, F, I, K, O, Q, S, V, Y	protein	54	Rhodobacter sphaeroides f. sp. denitrificans	Q3J1A4 (AlphaFold model)
Antenna pigment protein beta chain	B, E, G, J, N, P, R, T, W, Z	protein	48	Rhodobacter sphaeroides f. sp. denitrificans	Q3J1A3
PufX	X	protein	81	Rhodobacter sphaeroides f. sp. denitrificans	P13402

Sequence of entity 1 (L), FASTA

>7VY3_1 Photosynthetic reaction center L subunit (chains L)
ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWN
PQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFA
FAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAITFF
FTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSA
VFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING

Sequence of entity 2 (M), FASTA

>7VY3_2 Reaction center protein M chain (chains M)
AEYQNIFTQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSL
FSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASF
FMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIF
SHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIAD
RGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQN
HGMAPLN

Sequence of entity 3 (H), FASTA

>7VY3_3 Photosynthetic reaction center subunit H (chains H)
MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPK
PKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDL
PELDGHGHNKIKPMKAAAGFYVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLE
VELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGG
LMYAAPKRKSVVAAMLAEYA

Sequence of entity 4 (1, A, D, F, I, K, O, Q, S, V, Y), FASTA

>7VY3_4 Antenna pigment protein alpha chain (chains 1, A, D, F, I, K, O, Q, S, V, Y)
MSKFYKIWMIFDPRRVFVAQGVFLFLLAVMIHLILLSTPSYNWLEISAAKYNRV

Sequence of entity 5 (B, E, G, J, N, P, R, T, W, Z), FASTA

>7VY3_5 Antenna pigment protein beta chain (chains B, E, G, J, N, P, R, T, W, Z)
ADKSDLGYTGLTDEQAQELHSVYMSGLWLFSAVAIVAHLAVYIWRPWF

Sequence of entity 6 (X), FASTA

>7VY3_6 PufX (chains X)
ADKTIFNDHLNTNPKTNLRLWVAFQMMKGAGWAGGVFFGTLLLIGFFRVVGRMLPIDENP
APAPNITGALETGIELIKHLV

Ligands and cofactors

ID	Name	Formula	Copies
BCL	Bacteriochlorophyll a	C55 H74 Mg N4 O6	25
BPH	Bacteriopheophytin a	C55 H76 N4 O6	2
U10	Ubiquinone-10	C59 H90 O4	4
PGV	(1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoylo…	C40 H77 O10 P	8
LDA	Lauryl dimethylamine-N-oxide	C14 H31 N O	4
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	17
FE	FE (III) ion	Fe	1
SPO	Spheroidene	C41 H60 O	19
CDL	Cardiolipin	C81 H156 O17 P2	3
PTY	Phosphatidylethanolamine	C40 H80 N O8 P	2

Primary citation

Asymmetric structure of the native Rhodobacter sphaeroides dimeric LH1-RC complex. Tani, K., Kanno, R., Kikuchi, R. et al. Nat Commun (2022) 13:1904-1904. DOI 10.1038/s41467-022-29453-8 · PubMed

Other PDB entries of the same protein (UniProt P0C0Y8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7P0Q 1.73 Å, F(M197)H mutant structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides…
1RZH 1.8 Å, Photosynthetic reaction center double mutant from rhodobacter sphaeroides with asp L213…
2J8C 1.87 Å, X-ray high resolution structure of the photosynthetic reaction center from Rb.…
3I4D 2.01 Å, Photosynthetic reaction center from rhodobacter sphaeroides 2.4.1
2UWU 2.04 Å, X-ray high resolution structure of the photosynthetic reaction center from Rb.…
2UWW 2.05 Å, X-ray high resolution structure of the photosynthetic reaction center from Rb.…
2J8D 2.07 Å, X-ray high resolution structure of the photosynthetic reaction center from Rb.…
1QOV 2.1 Å, Photosynthetic reaction center mutant with ala M260 replaced with trp (chain M, A260W)
1RY5 2.1 Å, Photosynthetic reaction center mutant from rhodobacter sphaeroides with asp L213…
6Z02 2.1 Å, Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV in surfo…
6Z1J 2.1 Å, Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV LSP…
6Z27 2.1 Å, Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV LCP crystallization

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