6G7H: Bacteriorhodopsin

Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: resting state structure. Determined by X-ray diffraction at 1.5 Å resolution. Released 27 Jun 2018.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
Chains: 1
Atoms: 2,035
Mol. weight: 33 kDa
Ligands: RET, LI1, OLC
Released: 27 Jun 2018

Explore 6G7H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6G7H contains 13 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: 13 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	131-151	21
α-helix	152-156	5
α-helix	157-160	4
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	248	Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)	P02945 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6G7H_1 Bacteriorhodopsin (chains A)
QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSM
LLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIG
TGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVV
LWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSA
GDGAAATS

Ligands and cofactors

ID	Name	Formula	Copies
RET	Retinal	C20 H28 O	1
LI1	1-[2,6,10.14-tetramethyl-hexadecan-16-yl]-2-[2,10,14-trimethylhexadecan-16-yl]g…	C42 H86 O3	7
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	4

Primary citation

Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser. Nogly, P., Weinert, T., James, D. et al. Science (2018) 361. DOI 10.1126/science.aat0094 · 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…
7XJD 1.33 Å, Crystal structure of bacteriorhodopsin in the ground state by red laser irradiation
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

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