7XJD

Crystal structure of bacteriorhodopsin in the ground state by red laser irradiation

PDB DOI: https://doi.org/10.2210/pdb7XJD/pdb

Classification: PROTON TRANSPORT
Organism(s): Halobacterium salinarum NRC-1
Mutation(s): No
Membrane Protein: Yes PDBTMmpstruc

Deposited: 2022-04-16 Released: 2023-03-22
Deposition Author(s): Taguchi, S., Niwa, S., Takeda, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.176
R-Value Work: 0.136

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Detailed analysis of distorted retinal and its interaction with surrounding residues in the K intermediate of bacteriorhodopsin.

Taguchi, S., Niwa, S., Dao, H.A., Tanaka, Y., Takeda, R., Fukai, S., Hasegawa, K., Takeda, K.

(2023) Commun Biol 6: 190-190

PubMed: 36808185 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s42003-023-04554-2
Primary Citation of Related Structures:
7XJD

PubMed Abstract:
The K intermediate of proton pumping bacteriorhodopsin is the first intermediate generated after isomerization of retinal to the 13-cis form. Although various structures have been reported for the K intermediate until now, these differ from each other, especially in terms of the conformation of the retinal chromophore and its interaction with surrounding residues. We report here an accurate X-ray crystallographic analysis of the K structure. The polyene chain of 13-cis retinal is observed to be S-shaped. The side chain of Lys216, which is covalently bound to retinal via the Schiff-base linkage, interacts with residues, Asp85 and Thr89. In addition, the Nζ-H of the protonated Schiff-base linkage interacts with a residue, Asp212 and a water molecule, W402. Based on quantum chemical calculations for this K structure, we examine the stabilizing factors of distorted conformation of retinal and propose a relaxation manner to the next L intermediate.

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku, 606-8502, Japan.

Macromolecule Content

Total Structure Weight: 36.14 kDa
Atom Count: 2,313
Modelled Residue Count: 230
Deposited Residue Count: 230
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A	230	Halobacterium salinarum NRC-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)) Explore P02945 Go to UniProtKB: P02945
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02945
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L2P Query on L2P Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth A] SDF format, chain Q [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain C [auth A] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain C [auth A] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	2,3-DI-PHYTANYL-GLYCEROL C₄₃ H₈₈ O₃ ISDBCJSGCHUHFI-UMZPFTBHSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
SQU Query on SQU Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain H [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] mmCIF format, chain H [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A]	H [auth A], R [auth A], S [auth A], T [auth A]	2,10,23-TRIMETHYL-TETRACOSANE C₂₇ H₅₆ ZADHKSJXSZBQFB-HHHXNRCGSA-N		Interactions Focus chain H [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain H [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]
RET (Subject of Investigation/LOI) Query on RET Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]