6LM1 | pdb_00006lm1

The crystal structure of cyanorhodopsin (CyR) N4075R from cyanobacteria Tolypothrix sp. NIES-4075

• PDB DOI: https://doi.org/10.2210/pdb6LM1/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Tolypothrix sp. NIES-4075
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-24 Released: 2020-10-21 
• Deposition Author(s): Hosaka, T., Kimura-Someya, T., Shirouzu, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.204 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage.

Hasegawa, M., Hosaka, T., Kojima, K., Nishimura, Y., Nakajima, Y., Kimura-Someya, T., Shirouzu, M., Sudo, Y., Yoshizawa, S.

(2020) Sci Rep 10: 16752-16752

• PubMed: 33028840 
• DOI: https://doi.org/10.1038/s41598-020-73606-y
• Primary Citation Related Structures: 
  6LM0, 6LM1


• PubMed Abstract: 
  

  Microbial rhodopsin is a photoreceptor protein found in various bacteria and archaea, and it is considered to be a light-utilization device unique to heterotrophs. Recent studies have shown that several cyanobacterial genomes also include genes that encode rhodopsins, indicating that these auxiliary light-utilizing proteins may have evolved within photoautotroph lineages. To explore this possibility, we performed a large-scale genomic survey to clarify the distribution of rhodopsin and its phylogeny. Our surveys revealed a novel rhodopsin clade, cyanorhodopsin (CyR), that is unique to cyanobacteria. Genomic analysis revealed that rhodopsin genes show a habitat-biased distribution in cyanobacterial taxa, and that the CyR clade is composed exclusively of non-marine cyanobacterial strains. Functional analysis using a heterologous expression system revealed that CyRs function as light-driven outward H ⁺ pumps. Examination of the photochemical properties and crystal structure (2.65 Å resolution) of a representative CyR protein, N2098R from Calothrix sp. NIES-2098, revealed that the structure of the protein is very similar to that of other rhodopsins such as bacteriorhodopsin, but that its retinal configuration and spectroscopic characteristics (absorption maximum and photocycle) are distinct from those of bacteriorhodopsin. These results suggest that the CyR clade proteins evolved together with chlorophyll-based photosynthesis systems and may have been optimized for the cyanobacterial environment.

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Organizational Affiliation: 
• Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan.
Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8563, Japan.
Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Kanagawa, 230-0045, Japan.
Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, 305-8766, Japan.
Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan. [e-mail].
Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8563, Japan. [e-mail].
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 93.92 kDa 
• Atom Count: 6,037 
• Modeled Residue Count: 678 
• Deposited Residue Count: 777 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	A, B, C	259	Tolypothrix sp. NIES-4075	Mutation(s): 0  Gene Names: NIES4075_41530
UniProt
Find proteins for A0ACD6B9U0 (Tolypothrix sp. NIES-4075) Explore A0ACD6B9U0  Go to UniProtKB:  A0ACD6B9U0

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET (Subject of Investigation/LOI)	CA [auth B], D [auth A], WA [auth C]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
R16 (Subject of Investigation/LOI)	AA [auth A], OB [auth C], PB [auth C], QB [auth C], UA [auth B], W [auth A], X [auth A], Y [auth A], Z [auth A]	HEXADECANE C16 H34 DCAYPVUWAIABOU-UHFFFAOYSA-N
C14 (Subject of Investigation/LOI)	BA [auth A], TB [auth C], VA [auth B]	TETRADECANE C14 H30 BGHCVCJVXZWKCC-UHFFFAOYSA-N
D12 (Subject of Investigation/LOI)	NB [auth C], RA [auth B], SA [auth B], TA [auth B], U [auth A], V [auth A]	DODECANE C12 H26 SNRUBQQJIBEYMU-UHFFFAOYSA-N
D10 (Subject of Investigation/LOI)	PA [auth B], QA [auth B], S [auth A], T [auth A]	DECANE C10 H22 DIOQZVSQGTUSAI-UHFFFAOYSA-N
OCT (Subject of Investigation/LOI)	IB [auth C], JA [auth B], JB [auth C], K [auth A], KA [auth B], KB [auth C], L [auth A], LA [auth B], LB [auth C], M [auth A], MA [auth B], MB [auth C], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], Q [auth A], R [auth A]	N-OCTANE C8 H18 TVMXDCGIABBOFY-UHFFFAOYSA-N
HEX (Subject of Investigation/LOI)	AB [auth C], BB [auth C], CB [auth C], DB [auth C], EA [auth B], EB [auth C], F [auth A], FA [auth B], FB [auth C], G [auth A], GA [auth B], GB [auth C], H [auth A], HA [auth B], HB [auth C], I [auth A], IA [auth B], J [auth A], YA [auth C], ZA [auth C]	HEXANE C6 H14 VLKZOEOYAKHREP-UHFFFAOYSA-N
NO3 (Subject of Investigation/LOI)	RB [auth C], SB [auth C]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	DA [auth B], E [auth A], XA [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.204 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.92	α = 90
b = 129.666	β = 90
c = 127.626	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-21 
Deposition Author(s): Hosaka, T., Kimura-Someya, T., Shirouzu, M.

Revision History  

• Version 1.0: 2020-10-21
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary