4WD8 | pdb_00004wd8

Crystal structure of a bacterial Bestrophin homolog from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb4WD8/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Klebsiella pneumoniae UHKPC96
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-08 Released: 2014-10-01 
• Deposition Author(s): Yang, T., Liu, Q., Hendrickson, W.A., New York Consortium on Membrane Protein Structure (NYCOMPS)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.214 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Structure and selectivity in bestrophin ion channels.

Yang, T., Liu, Q., Kloss, B., Bruni, R., Kalathur, R.C., Guo, Y., Kloppmann, E., Rost, B., Colecraft, H.M., Hendrickson, W.A.

(2014) Science 346: 355-359

• PubMed: 25324390 
• DOI: https://doi.org/10.1126/science.1259723
• Primary Citation Related Structures: 
  4WD7, 4WD8


• PubMed Abstract: 
  

  Human bestrophin-1 (hBest1) is a calcium-activated chloride channel from the retinal pigment epithelium, where mutations are associated with vitelliform macular degeneration, or Best disease. We describe the structure of a bacterial homolog (KpBest) of hBest1 and functional characterizations of both channels. KpBest is a pentamer that forms a five-helix transmembrane pore, closed by three rings of conserved hydrophobic residues, and has a cytoplasmic cavern with a restricted exit. From electrophysiological analysis of structure-inspired mutations in KpBest and hBest1, we find a sensitive control of ion selectivity in the bestrophins, including reversal of anion/cation selectivity, and dramatic activation by mutations at the cytoplasmic exit. A homology model of hBest1 shows the locations of disease-causing mutations and suggests possible roles in regulation.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
New York Structural Biology Center, Synchrotron Beamlines, Brookhaven National Laboratory, Upton, NY 11973, USA.
New York Consortium on Membrane Protein Structure, New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA.
New York Consortium on Membrane Protein Structure, New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA. Department of Informatics, Bioinformatics and Computational Biology, TUM (Technische Universität München), Garching 85748, Germany.
Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. New York Structural Biology Center, Synchrotron Beamlines, Brookhaven National Laboratory, Upton, NY 11973, USA. New York Consortium on Membrane Protein Structure, New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA. Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Macromolecule Content 

• Total Structure Weight: 170.14 kDa 
• Atom Count: 11,016 
• Modeled Residue Count: 1,345 
• Deposited Residue Count: 1,485 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bestrophin domain protein	A, B, C, D, E	297	Klebsiella pneumoniae UHKPC96	Mutation(s): 0  Gene Names: H215_4284

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth C], N [auth C], O [auth C], P [auth D], Q [auth D], R [auth D], S [auth E], T [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.214 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.079	α = 90
b = 160.034	β = 90
c = 161.881	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-10-01 
Deposition Author(s): Yang, T., Liu, Q., Hendrickson, W.A., New York Consortium on Membrane Protein Structure (NYCOMPS)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM095315
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM107462

Revision History  

• Version 1.0: 2014-10-01
  Type: Initial release
  
• Version 1.1: 2014-10-29
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Refinement description