1R2N

NMR structure of the all-trans retinal in dark-adapted Bacteriorhodopsin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 12 
  • Selection Criteria: rms distance between observed and calculated chemical shifts 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structures of the active center in dark-adapted bacteriorhodopsin by solution-state NMR spectroscopy

Patzelt, H.Simon, B.terLaak, A.Kessler, B.Kuhne, R.Schmieder, P.Oesterhaelt, D.Oschkinat, H.

(2002) Proc Natl Acad Sci U S A 99: 9765-9770

  • DOI: https://doi.org/10.1073/pnas.132253899
  • Primary Citation of Related Structures:  
    1R2N, 1R84

  • PubMed Abstract: 

    The two forms of bacteriorhodopsin present in the dark-adapted state, containing either all-trans or 13-cis,15-syn retinal, were examined by using solution state NMR, and their structures were determined. Comparison of the all-trans and the 13-cis,15-syn forms shows a shift in position of about 0.25 A within the pocket of the protein. Comparing this to the 13-cis,15-anti chromophore of the catalytic cycle M-intermediate structure, the 13-cis,15-syn form demonstrates a less pronounced up-tilt of the retinal C12[bond]C14 region, while leaving W182 and T178 essentially unchanged. The N[bond]H dipole of the Schiff base orients toward the extracellular side in both forms, however, it reorients toward the intracellular side in the 13-cis,15-anti configuration to form the catalytic M-intermediate. Thus, the change of the N[bond]H dipole is considered primarily responsible for energy storage, conformation changes of the protein, and the deprotonation of the Schiff base. The structural similarity of the all-trans and 13-cis,15-syn forms is taken as strong evidence for the ion dipole dragging model by which proton (hydroxide ion) translocation follows the change of the dipole.


  • Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Membranbiochemie, Am Klopferspitz 18a, 82152 Martinsried, Germany;.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin249N/AMutation(s): 0 
Membrane Entity: Yes 
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download Ideal Coordinates CCD File 
B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 12 
  • Selection Criteria: rms distance between observed and calculated chemical shifts 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-28
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Data collection, Database references, Derived calculations