1E12 | pdb_00001e12

Halorhodopsin, a light-driven chloride pump

Experimental Data Snapshot

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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1E12

This is version 1.5 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: https://doi.org/10.1126/science.288.5470.1390
  • Primary Citation 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 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.

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

Macromolecule Content 

  • Total Structure Weight: 31.13 kDa 
  • Atom Count: 2,169 
  • Modeled Residue Count: 239 
  • Deposited Residue Count: 253 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HALORHODOPSIN253Halobacterium salinarumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0DMH7 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P0DMH7 
Go to UniProtKB:  P0DMH7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DMH7
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC

Query on OLC


Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
RET

Query on RET


Download:Ideal Coordinates CCD File
O [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
PLM

Query on PLM


Download:Ideal Coordinates CCD File
D [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
K

Query on K


Download:Ideal Coordinates CCD File
C [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

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

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-12-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.5: 2024-10-16
    Changes: Structure summary