1MGY | pdb_00001mgy

Structure of the D85S mutant of bacteriorhodopsin with bromide bound

• PDB DOI: https://doi.org/10.2210/pdb1MGY/pdb

• Classification: PROTON TRANSPORT
• Organism(s): Halobacterium salinarum
• Expression System: Halobacterium salinarum
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2002-08-16 Released: 2003-07-07 
• Deposition Author(s): Facciotti, M.T., Cheung, V.S., Nguyen, D., Rouhani, S., Glaeser, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.236 (Depositor) 
• R-Value Work: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Bromide-Bound D85S Mutant of Bacteriorhodopsin: Principles of Ion Pumping

Facciotti, M.T., Cheung, V.S., Nguyen, D., Rouhani, S., Glaeser, R.M.

(2003) Biophys J 85: 451-458

• PubMed: 12829500 
• DOI: https://doi.org/10.1016/S0006-3495(03)74490-7
• Primary Citation Related Structures: 
  1MGY


• PubMed Abstract: 
  

  We report the crystal structure of a bromide-bound form of the D85S mutant of bacteriorhodopsin, bR(D85S), a protein that uses light energy rather than ATP to pump halide ions across the cell membrane. Comparison of the structure of the halide-bound and halide-free states reveals that both displacements of individual side-chain positions and concerted helical movements occur on the extracellular side of the protein. Analysis of these structural changes reveals how this ion pump first facilitates ion uptake deep within the cell membrane and then prevents the backward escape of ions later in the pumping cycle. Together with the information provided by structures of intermediate states in the bacteriorhodopsin photocycle, this study also suggests the overall design principles that are necessary for ion pumping.

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Organizational Affiliation: 
• Graduate Group in Biophysics, University of California, Berkeley, California 94720, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.5 kDa 
• Atom Count: 1,819 
• Modeled Residue Count: 216 
• Deposited Residue Count: 249 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A	249	Halobacterium salinarum	Mutation(s): 1  Membrane Entity: Yes
UniProt
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)) Explore P02945  Go to UniProtKB:  P02945

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LI1	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL C42 H86 O3 YERVUJAKCNBGCR-BIHSMRAKSA-N
RET	E [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
BR	B [auth A], C [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.236 (Depositor) 
• R-Value Work:  0.215 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.498	α = 90
b = 121.326	β = 90
c = 73.875	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-07 
Deposition Author(s): Facciotti, M.T., Cheung, V.S., Nguyen, D., Rouhani, S., Glaeser, R.M.

Revision History  

• Version 1.0: 2003-07-07
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary