5X87

Crystal structure of a bacterial Bestrophin homolog from Klebsiella pneumoniae with a mutation L177T

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Klebsiella pneumoniae
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2017-03-01 Released: 2017-11-01 
  • Deposition Author(s): Zhang, Y., Chen, S., Yang, T.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States), National Institutes of Health/National Eye Institute (NIH/NEI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Patient-specific mutations impair BESTROPHIN1's essential role in mediating Ca2+-dependent Cl-currents in human RPE.

Li, Y.Zhang, Y.Xu, Y.Kittredge, A.Ward, N.Chen, S.Tsang, S.H.Yang, T.

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.29914
  • Primary Citation of Related Structures:  
    5X87

  • PubMed Abstract: 

    Mutations in the human BEST1 gene lead to retinal degenerative diseases displaying progressive vision loss and even blindness. BESTROPHIN1, encoded by BEST1 , is predominantly expressed in retinal pigment epithelium (RPE), but its physiological role has been a mystery for the last two decades. Using a patient-specific iPSC-based disease model and interdisciplinary approaches, we comprehensively analyzed two distinct BEST1 patient mutations, and discovered mechanistic correlations between patient clinical phenotypes, electrophysiology in their RPEs, and the structure and function of BESTROPHIN1 mutant channels. Our results revealed that the disease-causing mechanism of BEST1 mutations is centered on the indispensable role of BESTROPHIN1 in mediating the long speculated Ca 2+ -dependent Cl - current in RPE, and demonstrate that the pathological potential of BEST1 mutations can be evaluated and predicted with our iPSC-based 'disease-in-a-dish' approach. Moreover, we demonstrated that patient RPE is rescuable with viral gene supplementation, providing a proof-of-concept for curing BEST1 -associated diseases.


  • Organizational Affiliation

    Jonas Children's Vision Care, and Bernard and Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology and Pathology & Cell Biology, Edward S. Harkness Eye Institute, New York Presbyterian Hospital/Columbia University, New York, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bestrophin
A, B, C, D, E
297Klebsiella pneumoniaeMutation(s): 1 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth B]
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: 3.14 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.485α = 90
b = 160.573β = 90
c = 162.657γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103403
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesEY025290

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references
  • Version 1.2: 2018-02-28
    Changes: Database references
  • Version 1.3: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description