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 9T5R | pdb_00009t5r

LRR domain structure of the LRRC8D protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.226 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

Structures of the volume-regulated anion channel LRRC8A/D in activating and inhibiting conditions.

Lehmann, E.F., Stierli, F., Rutz, S., Deneka, D., Dutzler, R.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-77508-x
  • Primary Citation Related Structures: 
    9T5M, 9T5N, 9T5O, 9T5P, 9T5Q, 9T5R

  • PubMed Abstract: 

    Volume-regulated anion channels, which are activated in response to hypotonicity, are heteromers composed of LRRC8 family members. They consist of the obligatory subunit LRRC8A and at least another paralog that determines their substrate preference. Here we investigate heteromeric assemblies composed of LRRC8A and D subunits, the latter of which confer permeability to amino acids, osmolytes and anti-cancer drugs. Using patch-clamp electrophysiology, we show that LRRC8A/D channels are reversibly activated by cell swelling and that their response is modulated by sybodies targeting the A subunits, which either potentiate or repress channel activity. Structures of the LRRC8A/D channel in complex with the inhibitory sybody Sb1 define the channel stoichiometry of four A and two D subunits, with Sb1 stabilizing the A subunits in a similar closed channel conformation as found in homomeric LRRC8A assemblies. In LRRC8A/D heteromers, the two D subunits weaken the arrangement of A subunits and thus enhance the activation properties of the channel. This channel conformation is strongly perturbed upon binding of the potentiating sybody Sb4, which disrupts the packing of the cytoplasmic domains linking their mobility to pore opening.


  • Organizational Affiliation: 
    • Department of Biochemistry University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 47.2 kDa 
  • Atom Count: 3,643 
  • Modeled Residue Count: 406 
  • Deposited Residue Count: 411 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Volume-regulated anion channel subunit LRRC8D411Mus musculusMutation(s): 0 
Gene Names: Lrrc8d, Lrrc5
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CME
(Subject of Investigation/LOI)

Query on CME



Download:Ideal Coordinates CCD File
B [auth A]S,S-(2-HYDROXYETHYL)THIOCYSTEINE
C5 H11 N O3 S2
YPUBRSXDQSFQBA-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.226 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.855α = 90
b = 89.535β = 90
c = 143.698γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-02
    Type: Initial release
  • Version 1.1: 2026-09-30
    Changes: Database references