7XJD: Bacteriorhodopsin

Crystal structure of bacteriorhodopsin in the ground state by red laser irradiation. Determined by X-ray diffraction at 1.33 Å resolution. Released 22 Mar 2023.

Method: X-ray diffraction
Resolution: 1.33 Å
Organism: Halobacterium salinarum NRC-1
Chains: 1
Atoms: 2,313
Mol. weight: 36.14 kDa
Ligands: RET, SQU, L2P
Released: 22 Mar 2023

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

Secondary structure: helices and β-sheets

7XJD contains 11 α-helices and 2 β-strands across 1 chain. 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: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-30	21
α-helix	37-62	26
β-strand	66-71	6	1
β-strand	74-79	6	1
α-helix	81-100	20
α-helix	105-127	23
α-helix	131-154	24
α-helix	165-191	27
α-helix	201-213	13
α-helix	214-218	5
α-helix	219-224	6
α-helix	227-229	3
α-helix	231-232	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bacteriorhodopsin	A	protein	230	Halobacterium salinarum NRC-1	P02945 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7XJD_1 Bacteriorhodopsin (chains A)
TGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGY
GLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLV
GALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSA
YPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAE

Ligands and cofactors

ID	Name	Formula	Copies
RET	Retinal	C20 H28 O	1
SQU	2,10,23-trimethyl-tetracosane	C27 H56	4
L2P	2,3-di-phytanyl-glycerol	C43 H88 O3	14

Primary citation

Detailed analysis of distorted retinal and its interaction with surrounding residues in the K intermediate of bacteriorhodopsin. Taguchi, S., Niwa, S., Dao, H.A. et al. Commun Biol (2023) 6:190-190. DOI 10.1038/s42003-023-04554-2 · PubMed

Other PDB entries of the same protein (UniProt P02945 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z09 1.05 Å, Crystal structure of the ground state of bacteriorhodopsin at 1.05 Angstrom resolution
7Z0D 1.2 Å, Crystal structure of the L state of bacteriorhodopsin at 1.20 Angstrom resolution
7Z0A 1.22 Å, Crystal structure of the ground state of bacteriorhodopsin at 1.22 Angstrom resolution
7Z0E 1.22 Å, Crystal structure of the M state of bacteriorhodopsin at 1.22 Angstrom resolution
5ZIM 1.25 Å, Crystal structure of bacteriorhodopsin at 1.25 A resolution
5ZIN 1.27 Å, Crystal structure of bacteriorhodopsin at 1.27 A resolution
5ZIL 1.29 Å, Crystal structure of bacteriorhodopsin at 1.29 A resolution
7XJC 1.33 Å, Crystal structure of bacteriorhodopsin in the ground and K states after green laser…
7XJE 1.33 Å, Crystal structure of bacteriorhodopsin in the K state refined against the extrapolated…
1M0K 1.43 Å, Bacteriorhodopsin K intermediate at 1.43 a resolution
1M0M 1.43 Å, Bacteriorhodopsin M1 intermediate at 1.43 a resolution
9F9G 1.44 Å, Laser excitation effects on BR: Reprocessed Dark from Nogly et al.

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