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

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41598-020-73606-y
  • Primary Citation of 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.

  • Organizational Affiliation

    Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
259Tolypothrix sp. NIES-4075Mutation(s): 0 
Gene Names: NIES4075_41530
Membrane Entity: Yes 
Find proteins for A0A218QMM7 (Tolypothrix sp. NIES-4075)
Explore A0A218QMM7 
Go to UniProtKB:  A0A218QMM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A218QMM7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RET (Subject of Investigation/LOI)
Query on RET

Download Ideal Coordinates CCD File 
CA [auth B],
D [auth A],
WA [auth C]
C20 H28 O
R16 (Subject of Investigation/LOI)
Query on R16

Download Ideal Coordinates CCD File 
AA [auth A]
OB [auth C]
PB [auth C]
QB [auth C]
UA [auth B]
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]
C16 H34
C14 (Subject of Investigation/LOI)
Query on C14

Download Ideal Coordinates CCD File 
BA [auth A],
TB [auth C],
VA [auth B]
C14 H30
D12 (Subject of Investigation/LOI)
Query on D12

Download Ideal Coordinates CCD File 
NB [auth C]
RA [auth B]
SA [auth B]
TA [auth B]
U [auth A]
NB [auth C],
RA [auth B],
SA [auth B],
TA [auth B],
U [auth A],
V [auth A]
C12 H26
D10 (Subject of Investigation/LOI)
Query on D10

Download Ideal Coordinates CCD File 
PA [auth B],
QA [auth B],
S [auth A],
T [auth A]
C10 H22
OCT (Subject of Investigation/LOI)
Query on OCT

Download Ideal Coordinates CCD File 
IB [auth C]
JA [auth B]
JB [auth C]
K [auth A]
KA [auth B]
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]
C8 H18
HEX (Subject of Investigation/LOI)
Query on HEX

Download Ideal Coordinates CCD File 
AB [auth C]
BB [auth C]
CB [auth C]
DB [auth C]
EA [auth B]
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]
C6 H14
NO3 (Subject of Investigation/LOI)
Query on NO3

Download Ideal Coordinates CCD File 
RB [auth C],
SB [auth C]
N O3
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
DA [auth B],
E [auth A],
XA [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.92α = 90
b = 129.666β = 90
c = 127.626γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

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