8XX8

Structure of Glycilhalorhodopsin from Salinarimonas soli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Light-driven anion-pumping rhodopsin with unique cytoplasmic anion-release mechanism.

Ishizuka, T.Suzuki, K.Konno, M.Shibata, K.Kawasaki, Y.Akiyama, H.Murata, T.Inoue, K.

(2024) J Biol Chem 300: 107797-107797

  • DOI: https://doi.org/10.1016/j.jbc.2024.107797
  • Primary Citation of Related Structures:  
    8XX8

  • PubMed Abstract: 

    Microbial rhodopsins are photoreceptive membrane proteins found in microorganisms with an all-trans-retinal chromophore. The function of many microbial rhodopsins is determined by three residues in the third transmembrane helix called motif residues. Here, we report a group of microbial rhodopsins with a novel Thr-Thr-Gly (TTG) motif. The ion-transport assay revealed that they function as light-driven inward anion pumps similar to halorhodopsins previously found in archaea and bacteria. Based on the characteristic glycine residue in their motif and light-driven anion-pumping function, these new rhodopsins are called glycylhalorhodopsins (GHRs). X-ray crystallographic analysis found large cavities on the cytoplasmic side, which are produced by the small side-chain volume of the glycine residue in the motif. The opened structure of GHR on the cytoplasmic side is related to the anion releasing process to the cytoplasm during the photoreaction compared to canonical halorhodopsin from Natronomonas pharaonis (NpHR). GHR also transports SO 4 2- and the extracellular glutamate residue plays an essential role in extracellular SO 4 2- uptake. In summary, we have identified TTG motif-containing microbial rhodopsins that display an anion-releasing mechanism.


  • Organizational Affiliation

    The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rhodopsin263Salinarimonas soliMutation(s): 0 
Gene Names: F0L46_11385
Membrane Entity: Yes 
UniProt
Find proteins for A0A5B2VFD4 (Salinarimonas soli)
Explore A0A5B2VFD4 
Go to UniProtKB:  A0A5B2VFD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5B2VFD4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RET (Subject of Investigation/LOI)
Query on RET

Download Ideal Coordinates CCD File 
BB [auth F]
HA [auth D]
KB [auth C]
R [auth A]
RA [auth E]
BB [auth F],
HA [auth D],
KB [auth C],
R [auth A],
RA [auth E],
Y [auth B]
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
LFA
Query on LFA

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
G [auth A]
IA [auth E]
AA [auth D],
BA [auth D],
CA [auth D],
G [auth A],
IA [auth E],
S [auth B],
SA [auth F],
TA [auth F],
UA [auth F],
VA [auth F],
Z [auth D]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
OLA
Query on OLA

Download Ideal Coordinates CCD File 
AB [auth F]
DB [auth C]
EA [auth D]
EB [auth C]
FA [auth D]
AB [auth F],
DB [auth C],
EA [auth D],
EB [auth C],
FA [auth D],
FB [auth C],
GA [auth D],
GB [auth C],
HB [auth C],
I [auth A],
IB [auth C],
J [auth A],
JB [auth C],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
MA [auth E],
N [auth A],
NA [auth E],
O [auth A],
OA [auth E],
P [auth A],
PA [auth E],
Q [auth A],
QA [auth E],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
XA [auth F],
YA [auth F],
ZA [auth F]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
CB [auth C]
DA [auth D]
H [auth A]
JA [auth E]
T [auth B]
CB [auth C],
DA [auth D],
H [auth A],
JA [auth E],
T [auth B],
WA [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.22α = 90
b = 126.18β = 104.77
c = 97.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Database references