Structure of bacterorhodopsin mutant A51P

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 

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This is version 1.7 of the entry. See complete history


Proline substitutions are not easily accommodated in a membrane protein

Yohannan, S.Yang, D.Faham, S.Boulting, G.Whitelegge, J.Bowie, J.U.

(2004) J Mol Biol 341: 1-6

  • DOI: https://doi.org/10.1016/j.jmb.2004.06.025
  • Primary Citation of Related Structures:  
    1TN0, 1TN5

  • PubMed Abstract: 

    Proline residues are relatively common in transmembrane helices. This suggests that proline substitutions may be readily tolerated in membrane proteins, even though they invariably produce deviations from canonical helical structure. We have experimentally tested this possibility by making proline substitutions at 15 positions throughout the N-terminal half of bacteriorhodopsin helix B. We find that six of the substitutions yielded no active protein and all the others were destabilizing. Three mutations were only slightly destabilizing, however, reducing stability by about 0.5 kcal/mol, and these all occurred close to the N terminus. This result is consistent with the observation that proline is more common near the ends of TM helices. To learn how proline side-chains could be structurally accommodated at different locations in the helix, we solved the structures of a moderately destabilized mutant positioned near the N terminus of the helix, K41P, and a severely destabilized mutant positioned near the middle of the helix, A51P. The K41P mutation produced only local structural alterations, while the A51P mutation resulted in small, but widely distributed structural changes in helix B. Our results indicate that proline is not easily accommodated in transmembrane helices and that the tolerance to proline substitution is dependent, in a complex way, on the position in the structure.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, DOE Center for Genomics and Proteomics, Molecular Biology Institute, 655 Boyer Hall, 611 Charles E. Young Dr. E, University of California, Los Angeles, Los Angeles, CA 90095-1570, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
249Halobacterium salinarumMutation(s): 1 
Gene Names: BOPVNG1467G
Membrane Entity: Yes 
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P02945 
Go to UniProtKB:  P02945
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02945
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on RET

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C20 H28 O
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.105α = 90
b = 108.582β = 113.74
c = 55.821γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-02-01
    Changes: Structure summary
  • Version 1.4: 2018-01-24
    Changes: Structure summary
  • Version 1.5: 2018-01-31
    Changes: Experimental preparation
  • Version 1.6: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.7: 2023-08-23
    Changes: Data collection, Refinement description