9DX7 | pdb_00009dx7

LRRC8A:D Conformation 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Assembly and lipid-gating of LRRC8A:D volume-regulated anion channels.

Lurie, A.Stephens, C.A.Kern, D.M.Henn, K.M.Latorraca, N.R.Brohawn, S.G.

(2025) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-025-67052-5
  • Primary Citation of Related Structures:  
    9DX7, 9DXA

  • PubMed Abstract: 

    Volume-regulated anion channels (VRACs) are ubiquitously expressed vertebrate ion channels that open in response to hypotonic swelling. VRACs assemble as heteromers of LRRC8A and LRRC8B-E subunits, with different subunit combinations resulting in channels with different properties. Recent studies have described the structures of LRRC8A:C VRACs, but how other VRACs assemble, and which structural features are conserved or variant across channel assemblies remains unknown. Herein, we used cryo-EM to determine structures of a LRRC8A:D VRAC with a 4:2 subunit stoichiometry, which we captured in two conformations. The presence of LRRC8D subunits widens and increases hydrophobicity of the selectivity filter, which may contribute to the unique substrate selectivity of LRRC8D-containing VRACs. The structures reveal lipids bound inside the channel pore, similar to those observed in LRRC8A:C VRACs. We observe that LRRC8D subunit incorporation disrupts packing of the cytoplasmic LRR domains, increasing channel dynamics and opening lateral intersubunit gaps, which we speculate are necessary for pore lipid evacuation and channel activation. Molecular dynamics simulations show that lipids can reside stably within the pore to close the channel. Using electrophysiological experiments, we confirmed that pore lipids block conduction in the closed state, demonstrating that lipid-gating is a general property of VRACs.


  • Organizational Affiliation
    • Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Volume-regulated anion channel subunit LRRC8A,Soluble cytochrome b562A [auth C],
B [auth A],
C [auth B],
D
911Mus musculusMutation(s): 0 
Gene Names: Lrrc8aLrrc8cybCZ5846ECs5213
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE8 (Escherichia coli O157:H7)
Explore P0ABE8 
Go to UniProtKB:  P0ABE8
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 GroupsP0ABE8Q80WG5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Volume-regulated anion channel subunit LRRC8D
E, F
868Mus musculusMutation(s): 0 
Gene Names: Lrrc8dLrrc5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8BGR2 (Mus musculus)
Explore Q8BGR2 
Go to UniProtKB:  Q8BGR2
IMPC:  MGI:1922368
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8BGR2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEE
Query on PEE

Download Ideal Coordinates CCD File 
G [auth C]
H [auth C]
I [auth C]
J [auth C]
K [auth A]
G [auth C],
H [auth C],
I [auth C],
J [auth C],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth D],
S [auth D],
T [auth E],
U [auth E],
V [auth F],
W [auth F],
X [auth F]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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 States128263

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Data collection
  • Version 1.2: 2025-12-24
    Changes: Data collection, Database references