6NZW | pdb_00006nzw

LRRC8A-DCPIB in MSP1E3D1 nanodisc constricted state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6NZW

This is version 1.4 of the entry. See complete history

Literature

Cryo-EM structures of the DCPIB-inhibited volume-regulated anion channel LRRC8A in lipid nanodiscs.

Kern, D.M.Oh, S.Hite, R.K.Brohawn, S.G.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.42636
  • Primary Citation Related Structures: 
    6NZW, 6NZZ, 6O00

  • PubMed Abstract: 

    Hypoosmotic conditions activate volume-regulated anion channels in vertebrate cells. These channels are formed by leucine-rich repeat-containing protein 8 (LRRC8) family members and contain LRRC8A in homo- or hetero-hexameric assemblies. Here, we present single-particle cryo-electron microscopy structures of Mus musculus LRRC8A in complex with the inhibitor DCPIB reconstituted in lipid nanodiscs. DCPIB plugs the channel like a cork in a bottle - binding in the extracellular selectivity filter and sterically occluding ion conduction. Constricted and expanded structures reveal coupled dilation of cytoplasmic LRRs and the channel pore, suggesting a mechanism for channel gating by internal stimuli. Conformational and symmetry differences between LRRC8A structures determined in detergent micelles and lipid bilayers related to reorganization of intersubunit lipid binding sites demonstrate a critical role for the membrane in determining channel structure. These results provide insight into LRRC8 gating and inhibition and the role of lipids in the structure of an ionic-strength sensing ion channel.


  • Organizational Affiliation
    • Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, United States.

Macromolecule Content 

  • Total Structure Weight: 586 kDa 
  • Atom Count: 16,006 
  • Modeled Residue Count: 1,878 
  • Deposited Residue Count: 4,920 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Volume-regulated anion channel subunit LRRC8A
A, B, C, D, E
A, B, C, D, E, F
820Mus musculusMutation(s): 0 
Gene Names: Lrrc8aLrrc8
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q80WG5 (Mus musculus)
Explore Q80WG5 
Go to UniProtKB:  Q80WG5
IMPC:  MGI:2652847
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ80WG5
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV

Query on POV



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
K [auth B]
L [auth B]
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth C],
Q [auth D],
R [auth D],
S [auth D],
T [auth E],
U [auth E],
V [auth E],
W [auth F],
X [auth F],
Y [auth F]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
L9Y
(Subject of Investigation/LOI)

Query on L9Y



Download:Ideal Coordinates CCD File
J [auth A]4-{[(2S)-2-butyl-6,7-dichloro-2-cyclopentyl-1-oxo-2,3-dihydro-1H-inden-5-yl]oxy}butanoic acid
C22 H28 Cl2 O4
KHKGTPJPBOQECW-QFIPXVFZSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0

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 StatesDP2GM123496
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF32GM128263

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Other
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2025-06-04
    Changes: Data collection