5ETZ

Structure of the all-trans isomer of pharaonis halorhodopsin in the absence of halide ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.218 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Crystal Structure of the 11-cis Isomer of Pharaonis Halorhodopsin: Structural Constraints on Interconversions among Different Isomeric States

Chan, S.K.Kawaguchi, H.Kubo, H.Murakami, M.Ihara, K.Maki, K.Kouyama, T.

(2016) Biochemistry 55: 4092-4104

  • DOI: https://doi.org/10.1021/acs.biochem.6b00277
  • Primary Citation of Related Structures:  
    5B0W, 5ETZ

  • PubMed Abstract: 

    Like other microbial rhodopsins, the light driven chloride pump halorhodopsin from Natronomonas pharaonis (pHR) contains a mixture of all-trans/15-anti and 13-cis/15-syn isomers in the dark adapted state. A recent crystallographic study of the reaction states of pHR has shown that reaction states with 13-cis/15-syn retinal occur in the anion pumping cycle that is initiated by excitation of the all-trans isomer. In this study, we investigated interconversions among different isomeric states of pHR in the absence of chloride ions. The illumination of chloride free pHR with red light caused a large blue shift in the absorption maximum of the retinal visible band. During this "red adaptation", the content of the 11-cis isomer increased significantly, while the molar ratio of the 13-cis isomer to the all-trans isomer remained unchanged. The results suggest that the thermally activated interconversion between the 13-cis and the all-trans isomers is very rapid. Diffraction data from red adapted crystals showed that accommodation of the retinal chromophore with the 11-cis/15-syn configuration was achieved without a large change in the retinal binding pocket. The measurement of absorption kinetics under illumination showed that the 11-cis isomer, with a λmax at 565 nm, was generated upon excitation of a red-shifted species (λmax = 625 nm) that was present as a minor component in the dark adapted state. It is possible that this red-shifted species mimics an O-like reaction state with 13-cis/15-syn retinal, which was hypothesized to occur at a late stage of the anion pumping cycle.


  • Organizational Affiliation

    Department of Physics, Graduate School of Science, Nagoya University , Nagoya 464-8602, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HalorhodopsinA,
B,
C [auth D]
291Natronomonas pharaonis DSM 2160Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L3P
Query on L3P

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
L [auth B]
M [auth B]
Q [auth D]
F [auth A],
G [auth A],
L [auth B],
M [auth B],
Q [auth D],
R [auth D]
2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
C46 H94 O11 P2
TZXJQSKPTCRGCA-VZSPAKCESA-L
22B
Query on 22B

Download Ideal Coordinates CCD File 
E [auth A]BACTERIORUBERIN
C50 H76 O4
UVCQMCCIAHQDAF-CUMPQFAQSA-N
BNG
Query on BNG

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
N [auth B]
O [auth B]
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
S [auth D]
nonyl beta-D-glucopyranoside
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
RET
Query on RET

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B],
P [auth D]
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.4α = 90
b = 97.77β = 128.81
c = 101.62γ = 90
Software Package:
Software NamePurpose
CNSrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
XTALVIEWmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2016-07-27 
  • Deposition Author(s): Kouyama, T.

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2020-10-14
    Changes: Structure summary
  • Version 1.5: 2023-11-08
    Changes: Data collection, Database references, Refinement description