1BRR | pdb_00001brr

X-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX

PDB DOI: https://doi.org/10.2210/pdb1BRR/pdb

Classification: PROTON TRANSPORT
Organism(s): Halobacterium salinarum
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 1998-07-28 Released: 1998-09-30
Deposition Author(s): Essen, L.-O., Siegert, R., Oesterhelt, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.299 (Depositor), 0.301 (DCC)
R-Value Work:
0.256 (Depositor), 0.261 (DCC)
R-Value Observed:
0.256 (Depositor)

Starting Model: experimental
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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

PubMed: 9751724 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.95.20.11673
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 85.8 kDa
Atom Count: 5,672
Modeled Residue Count: 693
Deposited Residue Count: 741
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (BACTERIORHODOPSIN)	A, B, C	247	Halobacterium salinarum	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02945
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
3-O-sulfo-beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose	D, E	3		N/A	Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G37414ZM GlyCosmos: G37414ZM

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ARC Query on ARC Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	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		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]
RET Query on RET Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain S [auth C] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth C] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain S [auth C]	F [auth A], L [auth B], S [auth C]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain S [auth C]
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain W [auth C] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C]	J [auth A], R [auth B], W [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain R [auth B] Focus chain W [auth C] Interactions & Density Focus chain J [auth A] Focus chain R [auth B] Focus chain W [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A, B, C	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.299 (Depositor), 0.301 (DCC)
R-Value Work: 0.256 (Depositor), 0.261 (DCC)
R-Value Observed: 0.256 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.52	α = 90
b = 105.96	β = 94.94
c = 80.19	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 1998-09-30

Deposition Author(s):

Essen, L.-O.

Siegert, R.

Oesterhelt, D.

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