2GNU: Reaction center protein H chain

The crystallization of reaction center from Rhodobacter sphaeroides occurs via a new route. Determined by X-ray diffraction at 2.2 Å resolution. Released 7 Nov 2006.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Rhodobacter sphaeroides
Chains: 3
Atoms: 7,045
Mol. weight: 99.45 kDa
Ligands: LDA, BCL, U10, FE2
Released: 7 Nov 2006

Explore 2GNU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2GNU contains 52 α-helices and 30 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 H: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
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	2
β-strand	72-75	4	2
β-strand	87-88	2	3
β-strand	99-100	2	3
α-helix	104-107	4
α-helix	110-112	3
α-helix	121-122	2
β-strand	123	1	4
β-strand	129	1	4
β-strand	131-133	3	5
α-helix	134-136	3
β-strand	141-144	4	6
α-helix	151	1
β-strand	152-155	4	5
β-strand	160-170	11	5
β-strand	175-183	9	5
β-strand	188-192	5	5
α-helix	193-195	3
β-strand	197-198	2	5
β-strand	203-205	3	5
α-helix	217-219	3
α-helix	227-243	17

Chain L: 19 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
α-helix	7-9	3
β-strand	25-26	2	7
β-strand	29-30	2	7
α-helix	33-56	24
β-strand	65-66	2	8
α-helix	67-70	4
α-helix	71-73	3
α-helix	80-82	3
α-helix	84-111	28
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	8
α-helix	152-163	12
α-helix	167-169	3
α-helix	171-198	28
α-helix	209-220	12
α-helix	226-249	24
β-strand	251	1	9
β-strand	255	1	9
α-helix	259-263	5
α-helix	264-267	4
α-helix	272-274	3

Chain M: 22 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	6
α-helix	16-17	2
α-helix	26-28	3
β-strand	29	1	10
α-helix	37-40	4
β-strand	51	1	10
α-helix	54-77	24
α-helix	82-88	7
β-strand	94	1	11
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
α-helix	175-176	2
β-strand	177	1	11
α-helix	179-192	14
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	265-285	21
β-strand	287	1	12
β-strand	291	1	12
α-helix	294-299	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Reaction center protein H chain	H	protein	235	Rhodobacter sphaeroides	P0C0Y7 (AlphaFold model)
Reaction center protein L chain	L	protein	281	Rhodobacter sphaeroides	P0C0Y8 (AlphaFold model)
Reaction center protein M chain	M	protein	300	Rhodobacter sphaeroides	P0C0Y9 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>2GNU_1 Reaction center protein H chain (chains H)
DLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGR
GTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNK
IKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRL
LPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAA

Sequence of entity 2 (L), FASTA

>2GNU_2 Reaction center protein L chain (chains L)
ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWN
PQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFA
FAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFF
FTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSA
VFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING

Sequence of entity 3 (M), FASTA

>2GNU_3 Reaction center protein M chain (chains M)
EYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLF
SGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFF
MFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFS
HLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADR
GTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNH

Ligands and cofactors

ID	Name	Formula	Copies
LDA	Lauryl dimethylamine-N-oxide	C14 H31 N O	1
BCL	Bacteriochlorophyll a	C55 H74 Mg N4 O6	4
U10	Ubiquinone-10	C59 H90 O4	2
FE2	FE (II) ion	Fe	1
BPH	Bacteriopheophytin a	C55 H76 N4 O6	2
CDL	Cardiolipin	C81 H156 O17 P2	1

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

Primary citation

Lipidic sponge phase crystallization of membrane proteins. Wadsten, P., Woehri, A.B., Snijder, A. et al. J Mol Biol (2006) 364:44-53. DOI 10.1016/j.jmb.2006.06.043 · PubMed

Other PDB entries of the same protein (UniProt P0C0Y7 (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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