1BRR

X-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.256 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.2 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 U S A 95: 11673-11678

  • DOI: https://doi.org/10.1073/pnas.95.20.11673
  • Primary Citation of Related Structures:  
    1BRR

  • 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 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.

    • Organizational Affiliation: 

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


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (BACTERIORHODOPSIN)
A, B, C
247Halobacterium salinarumMutation(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
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
3-O-sulfo-beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose
D, E
3N/A
Glycosylation Resources
GlyTouCan:  G37414ZM
GlyCosmos:  G37414ZM
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ARC
Query on ARC
Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
M [auth B]
N [auth B]
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
T [auth C],
U [auth C],
V [auth C]
3,7,11,15-TETRAMETHYL-HEXADECAN-1-OL
C20 H42 O
AJAKLDUGVSKVDG-UFYCRDLUSA-N
RET
Query on RET
Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
S [auth C]		RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
BGC
Query on BGC
Download Ideal Coordinates CCD File 
K [auth B]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
OCT
Query on OCT
Download Ideal Coordinates CCD File 
Q [auth B]N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
J [auth A],
R [auth B],
W [auth C]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A, B, C
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.256 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.52α = 90
b = 105.96β = 94.94
c = 80.19γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-09-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 3.2: 2024-11-20
    Changes: Structure summary