5ZIM: Bacteriorhodopsin

Crystal structure of bacteriorhodopsin at 1.25 A resolution. Determined by X-ray diffraction at 1.25 Å resolution. Released 10 Oct 2018.

Method: X-ray diffraction
Resolution: 1.25 Å
Organism: Halobacterium salinarum
Chains: 1
Atoms: 2,038
Mol. weight: 27.89 kDa
Ligands: RET, L2P
Released: 10 Oct 2018

Explore 5ZIM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ZIM contains 10 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: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-31	22
α-helix	37-61	25
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	201-212	12
α-helix	213-218	6
α-helix	219-224	6
α-helix	227-229	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bacteriorhodopsin	A	protein	228	Halobacterium salinarum	P02945 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5ZIM_1 Bacteriorhodopsin (chains A)
TGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGY
GLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLV
GALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSA
YPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE

Ligands and cofactors

ID	Name	Formula	Copies
RET	Retinal	C20 H28 O	1
L2P	2,3-di-phytanyl-glycerol	C43 H88 O3	4

Primary citation

X-ray structure analysis of bacteriorhodopsin at 1.3 angstrom resolution. Hasegawa, N., Jonotsuka, H., Miki, K. et al. Sci Rep (2018) 8:13123-13123. DOI 10.1038/s41598-018-31370-0 · 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
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
9F9G 1.44 Å, Laser excitation effects on BR: Reprocessed Dark from Nogly et al.

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