3VVK

An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.211 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Large deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide

Nakanishi, T.Kanada, S.Murakami, M.Ihara, K.Kouyama, T.

(2013) Biophys J 104: 377-385

  • DOI: https://doi.org/10.1016/j.bpj.2012.12.018
  • Primary Citation of Related Structures:  
    3VVK

  • PubMed Abstract: 

    Halorhodopsin from Natronomonas pharaonis (pHR), a retinylidene protein that functions as a light-driven chloride ion pump, is converted into a proton pump in the presence of azide ion. To clarify this conversion, we investigated light-induced structural changes in pHR using a C2 crystal that was prepared in the presence of Cl(-) and subsequently soaked in a solution containing azide ion. When the pHR-azide complex was illuminated at pH 9, a profound outward movement (∼4 Å) of the cytoplasmic half of helix F was observed in a subunit with the EF loop facing an open space. This movement created a long water channel between the retinal Schiff base and the cytoplasmic surface, along which a proton could be transported. Meanwhile, the middle moiety of helix C moved inward, leading to shrinkage of the primary anion-binding site (site I), and the azide molecule in site I was expelled out to the extracellular medium. The results suggest that the cytoplasmic half of helix F and the middle moiety of helix C act as different types of valves for active proton transport.


  • Organizational Affiliation

    Graduate School of Science, Nagoya University, Nagoya, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Halorhodopsin
A, B, C, D, E
A, B, C, D, E, F
291Natronomonas pharaonisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P15647 (Natronomonas pharaonis)
Explore P15647 
Go to UniProtKB:  P15647
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15647
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L3P
Query on L3P

Download Ideal Coordinates CCD File 
N [auth C],
O [auth C],
Q [auth D],
V [auth E]
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 
M [auth C],
U [auth E]
BACTERIORUBERIN
C50 H76 O4
UVCQMCCIAHQDAF-CUMPQFAQSA-N
BNG
Query on BNG

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H [auth A],
I [auth A],
K [auth B],
S [auth D]
nonyl beta-D-glucopyranoside
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
RET
Query on RET

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G [auth A]
J [auth B]
L [auth C]
P [auth D]
T [auth E]
G [auth A],
J [auth B],
L [auth C],
P [auth D],
T [auth E],
X [auth F]
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
AZI
Query on AZI

Download Ideal Coordinates CCD File 
R [auth D],
W [auth E],
Y [auth F]
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.85α = 90
b = 97.9β = 128.53
c = 101.02γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary