4QRY

the ground state and the N intermediate of pharaonis halorhodopsin in complex with bromide ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of the L1, L2, N, and O States of pharaonis Halorhodopsin

Kouyama, T.Kawaguchi, H.Nakanishi, T.Kubo, H.Murakami, M.

(2015) Biophys J 108: 2680-2690

  • DOI: https://doi.org/10.1016/j.bpj.2015.04.027
  • Primary Citation of Related Structures:  
    4QRY

  • PubMed Abstract: 

    Halorhodopsin from Natronomonas pharaonis (pHR) functions as a light-driven halide ion pump. In the presence of halide ions, the photochemical reaction of pHR is described by the scheme: K→ L1 → L2 → N → O → pHR' → pHR. Here, we report light-induced structural changes of the pHR-bromide complex observed in the C2 crystal. In the L1-to-L2 transition, the bromide ion that initially exists in the extracellular vicinity of retinal moves across the retinal Schiff base. Upon the formation of the N state with a bromide ion bound to the cytoplasmic vicinity of the retinal Schiff base, the cytoplasmic half of helix F moves outward to create a water channel in the cytoplasmic interhelical space, whereas the extracellular half of helix C moves inward. During the transition from N to an N-like reaction state with retinal assuming the 13-cis/15-syn configuration, the translocated bromide ion is released into the cytoplasmic medium. Subsequently, helix F relaxes into its original conformation, generating the O state. Anion uptake from the extracellular side occurs when helix C relaxes into its original conformation. These structural data provide insight into the structural basis of unidirectional anion transport.


  • Organizational Affiliation

    Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan; RIKEN Harima Branch, 1-1-1, Kouto, Sayo, Hyogo, Japan. Electronic address: kouyama@bio.phys.nagoya-u.ac.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Halorhodopsin291Natronomonas pharaonisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L2P
Query on L2P

Download Ideal Coordinates CCD File 
AA [auth F]
FA [auth G]
R [auth C]
V [auth E]
Y [auth F]
AA [auth F],
FA [auth G],
R [auth C],
V [auth E],
Y [auth F],
Z [auth F]
2,3-DI-PHYTANYL-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
BNG
Query on BNG

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J [auth A],
K [auth B],
S [auth E],
T [auth E],
U [auth E]
nonyl beta-D-glucopyranoside
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
RET
Query on RET

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CA [auth F]
G [auth A]
GA [auth G]
L [auth B]
O [auth C]
CA [auth F],
G [auth A],
GA [auth G],
L [auth B],
O [auth C],
W [auth E]
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
BR
Query on BR

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BA [auth F]
DA [auth F]
EA [auth F]
H [auth A]
HA [auth G]
BA [auth F],
DA [auth F],
EA [auth F],
H [auth A],
HA [auth G],
I [auth A],
IA [auth G],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
X [auth E]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.36α = 90
b = 98.3β = 128.13
c = 100.53γ = 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: 2015-06-17
    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