2KSY | pdb_00002ksy

Solution nmr structure of sensory rhodopsin II

• PDB DOI: https://doi.org/10.2210/pdb2KSY/pdb
• BMRB: 16678

• Classification: MEMBRANE PROTEIN
• Organism(s): Natronomonas pharaonis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-14 Released: 2010-06-02 
• Deposition Author(s): Gautier, A., Mott, H.R., Bostock, M.J., Kirkpatrick, J.P., Nietlispach, D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 

Literature

Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy.

Gautier, A., Mott, H.R., Bostock, M.J., Kirkpatrick, J.P., Nietlispach, D.

(2010) Nat Struct Mol Biol 17: 768-774

• PubMed: 20512150 
• DOI: https://doi.org/10.1038/nsmb.1807
• Primary Citation Related Structures: 
  2KSY


• PubMed Abstract: 
  

  Seven-helix membrane proteins represent a challenge for structural biology. Here we report the first NMR structure determination of a detergent-solubilized seven-helix transmembrane (7TM) protein, the phototaxis receptor sensory rhodopsin II (pSRII) from Natronomonas pharaonis, as a proof of principle. The overall quality of the structure ensemble is good (backbone r.m.s. deviation of 0.48 A) and agrees well with previously determined X-ray structures. Furthermore, measurements in more native-like small phospholipid bicelles indicate that the protein structure is the same as in detergent micelles, suggesting that environment-specific effects are minimal when using mild detergents. We use our case study as a platform to discuss the feasibility of similar solution NMR studies for other 7TM proteins, including members of the family of G protein-coupled receptors.

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Organizational Affiliation: 
• Department of Biochemistry, University of Cambridge, Cambridge, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.74 kDa 
• Atom Count: 1,891 
• Modeled Residue Count: 247 
• Deposited Residue Count: 247 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensory rhodopsin II	A	247	Natronomonas pharaonis	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET	B [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-02 
Deposition Author(s): Gautier, A., Mott, H.R., Bostock, M.J., Kirkpatrick, J.P., Nietlispach, D.

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2015-06-10
  Changes: Non-polymer description, Structure summary
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary