6LM1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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


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

  • 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

    Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Kanagawa, 230-0045, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rhodopsin
A, B, C
259Tolypothrix sp. NIES-4075Mutation(s): 0 
Gene Names: NIES4075_41530
Membrane Entity: Yes 
UniProt
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
Expand
  • 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]
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
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]
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
C14 (Subject of Investigation/LOI)
Query on C14

Download Ideal Coordinates CCD File 
BA [auth A],
TB [auth C],
VA [auth B]
TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
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]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
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]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
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]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
HEX (Subject of Investigation/LOI)
Query on HEX

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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]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
NO3 (Subject of Investigation/LOI)
Query on NO3

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RB [auth C],
SB [auth C]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
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 
  • 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
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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