1E12

Halorhodopsin, a light-driven chloride pump


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of Light-Driven Chloride Pump Halorhodopsin at 1.8 A Resolution

Kolbe, M.Besir, H.Essen, L.-O.Oesterhelt, D.

(2000) Science 288: 1390

  • DOI: 10.1126/science.288.5470.1390
  • Primary Citation of Related Structures:  
    1E12

  • PubMed Abstract: 
  • Halorhodopsin, an archaeal rhodopsin ubiquitous in Haloarchaea, uses light energy to pump chloride through biological membranes. Halorhodopsin crystals were grown in a cubic lipidic phase, which allowed the x-ray structure determination of this anion ...

    Halorhodopsin, an archaeal rhodopsin ubiquitous in Haloarchaea, uses light energy to pump chloride through biological membranes. Halorhodopsin crystals were grown in a cubic lipidic phase, which allowed the x-ray structure determination of this anion pump at 1.8 angstrom resolution. Halorhodopsin assembles to trimers around a central patch consisting of palmitic acid. Next to the protonated Schiff base between Lys(242) and the isomerizable retinal chromophore, a single chloride ion occupies the transport site. Energetic calculations on chloride binding reveal a combination of ion-ion and ion-dipole interactions for stabilizing the anion 18 angstroms below the membrane surface. Ion dragging across the protonated Schiff base explains why chloride and proton translocation modes are mechanistically equivalent in archaeal rhodopsins.


    Related Citations: 
    • The Structure and Mechanism of the Family of Retinal Proteins from Halophilic Archaea
      Oesterhelt, D.
      (1998) Curr Opin Struct Biol 8: 489
    • Three-Dimensional Structure of Halorhodopsin at 7 Angstrom Resolution
      Havelka, W., Henderson, R., Oesterhelt, D.
      (1995) J Mol Biol 247: 726

    Organizational Affiliation

    Department of Membrane Biochemistry, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18a, D-82152 Martinsried bei München, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HALORHODOPSINA253Halobacterium salinarumMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial, Algal, and viral Rhodopsins
Protein: 
Halorhodopsin (HR)
Find proteins for P0DMH7 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P0DMH7 
Go to UniProtKB:  P0DMH7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
RET
Query on RET

Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
PLM
Query on PLM

Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.3α = 90
b = 67.3β = 90
c = 209.2γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-02
    Type: Initial release
  • Version 1.1: 2012-11-14
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2016-02-03
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2019-05-22
    Changes: Advisory, Data collection, Derived calculations, Experimental preparation, Other