1GUE | pdb_00001gue

SENSORY RHODOPSIN II

• PDB DOI: https://doi.org/10.2210/pdb1GUE/pdb

• Classification: PHOTORECEPTOR
• Organism(s): Natronomonas pharaonis
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2002-01-24 Released: 2002-04-12 
• Deposition Author(s): Edman, K., Royant, A., Nollert, P., Maxwell, C.A., Pebay-Peyroula, E., Navarro, J., Neutze, R., Landau, E.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.311 (Depositor) 
• R-Value Work: 
  0.277 (Depositor) 
• R-Value Observed: 
  0.277 (Depositor) 

Starting Model: experimental

Literature

Early Structural Rearrangements in the Photocycle of an Integral Membrane Sensory Receptor

Edman, K., Royant, A., Nollert, P., Maxwell, C.A., Pebay-Peyroula, E., Navarro, J., Neutze, R., Landau, E.M.

(2002) Structure 10: 473

• PubMed: 11937052 
• DOI: https://doi.org/10.1016/s0969-2126(02)00736-0
• Primary Citation Related Structures: 
  1GU8, 1GUE


• PubMed Abstract: 
  

  Sensory rhodopsins are the primary receptors of vision in animals and phototaxis in microorganisms. Light triggers the rapid isomerization of a buried retinal chromophore, which the protein both accommodates and amplifies into the larger structural rearrangements required for signaling. We trapped an early intermediate of the photocycle of sensory rhodopsin II from Natronobacterium pharaonis (pSRII) in 3D crystals and determined its X-ray structure to 2.3 A resolution. The observed structural rearrangements were localized near the retinal chromophore, with a key water molecule becoming disordered and the retinal's beta-ionone ring undergoing a prominent movement. Comparison with the early structural rearrangements of bacteriorhodopsin illustrates how modifications in the retinal binding pocket of pSRII allow subtle differences in the early relaxation of photoisomerized retinal.

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Organizational Affiliation: 
• Department of Molecular Biotechnology, Chalmers University of Technology, Box 462, S-40530 Gothenburg, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 25.69 kDa 
• Atom Count: 1,660 
• Modeled Residue Count: 218 
• Deposited Residue Count: 239 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SENSORY RHODOPSIN II	A	239	Natronomonas pharaonis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P42196 (Natronomonas pharaonis) Explore P42196  Go to UniProtKB:  P42196

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET	B [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.311 (Depositor) 
• R-Value Work:  0.277 (Depositor) 
• R-Value Observed: 0.277 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.51	α = 90
b = 128.553	β = 90
c = 50.799	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-04-12 
Deposition Author(s): Edman, K., Royant, A., Nollert, P., Maxwell, C.A., Pebay-Peyroula, E., Navarro, J., Neutze, R., Landau, E.M.

Revision History  

• Version 1.0: 2002-04-12
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary