9KP6 | pdb_00009kp6

Cryo-EM structure of mouse bestrophin-1 in a closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures of mouse bestrophin 1 channel in closed and partially open conformations.

Kim, K.W.Lee, E.Ko, A.Hwang, J.Park, K.Lee, B.C.Kim, K.W.Oh, W.J.Kim, K.Lim, H.H.

(2025) Mol Cells 48: 100208-100208

  • DOI: https://doi.org/10.1016/j.mocell.2025.100208
  • Primary Citation of Related Structures:  
    9KC9, 9KCA, 9KP6

  • PubMed Abstract: 

    Bestrophin-1 (BEST1) channels are calcium-activated Cl - channels involved in diverse physiological processes, including gliotransmitter release in astrocytes. Although human and chicken BEST1 orthologs have been extensively studied, the structural and functional properties of mouse BEST1 (mBEST1) remain poorly understood. In this study, we characterized the structure-function of mBEST1-BF, a C-terminally tagged variant, using whole-cell patch-clamp recordings, surface biotinylation assays, and single-particle cryo-electron microscopy (cryo-EM). Cryo-EM structural analysis of mBEST1-BF revealed closed and partially open conformations. Comparative analysis with human and chicken BEST1 orthologs highlighted conserved calcium-binding and gating mechanisms, with distinct features in mBEST1, including a wider aperture sufficient to accommodate dehydrated Cl - ions and potential anion-binding sites near Val205 and Gln208 residues. The disordered C-terminal region of mBEST1 remains unresolved, suggesting it may require stabilizing factors for structural determination. Additionally, the autoinhibitory domain, which includes Ser354, likely plays a key role in regulating gating, with Ser354 potentially serving as a phosphorylation site that modulates channel activity. Our findings provide structural and functional insights into mBEST1 and suggest mechanisms underlying its unique gating and ion permeation properties.


  • Organizational Affiliation
    • Neurovascular Unit Research Group, Korea Brain Research Institute (KBRI), Daegu, 41068, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bestrophin-1,Soluble cytochrome b562
A, B, C, D, E
689Mus musculusMutation(s): 3 
Gene Names: Best1Bmd1Vmd2cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O76090 (Homo sapiens)
Explore O76090 
Go to UniProtKB:  O76090
PHAROS:  O76090
GTEx:  ENSG00000167995 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76090
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D],
S [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
J [auth B]
K [auth B]
M [auth C]
G [auth A],
H [auth A],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
P [auth D],
Q [auth D],
R [auth E],
T [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5156:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2021R1A2C1004884
National Research Foundation (NRF, Korea)Korea, Republic Of2020 M3E5D907

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Data collection, Database references