4OV0 | pdb_00004ov0

Structure of Bacteriorhdopsin Transferred from Amphipol A8-35 to a Lipidic Mesophase

• PDB DOI: https://doi.org/10.2210/pdb4OV0/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Halobacterium salinarum NRC-1
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2014-02-19 Released: 2014-10-01 
• Deposition Author(s): Polovinkin, V., Gushchin, I., Sintsov, M., Round, E., Balandin, T., Chervakov, P., Schevchenko, V., Utrobin, P., Popov, A., Borshchevskiy, V., Mishin, A., Kuklin, A., Willbold, D., Popot, J.L., Gordeliy, V.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.209 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

High-resolution structure of a membrane protein transferred from amphipol to a lipidic mesophase.

Polovinkin, V., Gushchin, I., Sintsov, M., Round, E., Balandin, T., Chervakov, P., Schevchenko, V., Utrobin, P., Popov, A., Borshchevskiy, V., Mishin, A., Kuklin, A., Willbold, D., Chupin, V., Popot, J.L., Gordeliy, V.

(2014) J Membr Biol 247: 997-1004

• PubMed: 25192977 
• DOI: https://doi.org/10.1007/s00232-014-9700-x
• Primary Citation Related Structures: 
  4OV0


• PubMed Abstract: 
  

  Amphipols (APols) have become important tools for the stabilization, folding, and in vitro structural and functional studies of membrane proteins (MPs). Direct crystallization of MPs solubilized in APols would be of high importance for structural biology. However, despite considerable efforts, it is still not clear whether MP/APol complexes can form well-ordered crystals suitable for X-ray crystallography. In the present work, we show that an APol-trapped MP can be crystallized in meso. Bacteriorhodopsin (BR) trapped by APol A8-35 was mixed with a lipidic mesophase, and crystallization was induced by adding a precipitant. The crystals diffract beyond 2 Å. The structure of BR was solved to 2 Å and found to be indistinguishable from previous structures obtained after transfer from detergent solutions. We suggest the proposed protocol of in meso crystallization to be generally applicable to APol-trapped MPs.

---

Organizational Affiliation: 
• Univ. Grenoble Alpes, IBS, 38044, Grenoble, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.21 kDa 
• Atom Count: 1,695 
• Modeled Residue Count: 214 
• Deposited Residue Count: 249 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A	249	Halobacterium salinarum NRC-1	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET	B [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.209 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.999	α = 90
b = 60.999	β = 90
c = 108.174	γ = 120

Software Package:

Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-01 
Deposition Author(s): Polovinkin, V., Gushchin, I., Sintsov, M., Round, E., Balandin, T., Chervakov, P., Schevchenko, V., Utrobin, P., Popov, A., Borshchevskiy, V., Mishin, A., Kuklin, A., Willbold, D., Popot, J.L., Gordeliy, V.

Revision History  

• Version 1.0: 2014-10-01
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary