1BRR

X-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex

Essen, L.Siegert, R.Lehmann, W.D.Oesterhelt, D.

(1998) Proc.Natl.Acad.Sci.USA 95: 11673-11678


  • PubMed Abstract: 
  • Heterogenous nucleation on small molecule crystals causes a monoclinic crystal form of bacteriorhodopsin (BR) in which trimers of this membrane protein pack differently than in native purple membranes. Analysis of single crystals by nano-electrospray ...

    Heterogenous nucleation on small molecule crystals causes a monoclinic crystal form of bacteriorhodopsin (BR) in which trimers of this membrane protein pack differently than in native purple membranes. Analysis of single crystals by nano-electrospray ionization-mass spectrometry demonstrated a preservation of the purple membrane lipid composition in these BR crystals. The 2.9-A x-ray structure shows a lipid-mediated stabilization of BR trimers where the glycolipid S-TGA-1 binds into the central compartment of BR trimers. The BR trimer/lipid complex provides an example of local membrane thinning as the lipid head-group boundary of the central lipid patch is shifted by 5 A toward the membrane center. Nonbiased electron density maps reveal structural differences to previously reported BR structures, especially for the cytosolic EF loop and the proton exit pathway. The terminal proton release complex now comprises an E194-E204 dyad as a diffuse proton buffer.


    Related Citations: 
    • Orthorhombic Crystal Form of Bacteriorhodopsin Nucleated on Benzamidine Diffracting to 3.6 Angstrom Resolution
      Schertler, G.F.X.,Bartunik, H.D.,Michel, H.,Oesterhelt, D.
      (1993) J.Mol.Biol. 234: 156


    Organizational Affiliation

    Max-Planck-Institut fur Biochemie, Am Klopferspitz 18a, D-82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (BACTERIORHODOPSIN)
A, B, C
247Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)Mutation(s): 0 
Gene Names: bop
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial and Algal Rhodopsins
Protein: 
Bacteriorhodopsin (BR)
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Go to UniProtKB:  P02945
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SGA
Query on SGA

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B, C
O3-SULFONYLGALACTOSE
C6 H12 O9 S
HHRMGTRTCHNCRO-FDROIEKHSA-N
 Ligand Interaction
OCT
Query on OCT

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Download CCD File 
B
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
ARC
Query on ARC

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Download CCD File 
A, B, C
3,7,11,15-TETRAMETHYL-HEXADECAN-1-OL
C20 H42 O
AJAKLDUGVSKVDG-UFYCRDLUSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
B, C
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BGC
Query on BGC

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B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
RET
Query on RET

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A, B, C
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
GLC
Query on GLC

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B, C
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B, C
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.256 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 120.520α = 90.00
b = 105.960β = 94.94
c = 80.190γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
DENZOdata reduction
X-PLORmodel building
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-09-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance