[English] 日本語
Yorodumi
- PDB-6fnw: Structure of a volume-regulated anion channel of the LRRC8 family -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fnw
TitleStructure of a volume-regulated anion channel of the LRRC8 family
ComponentsVolume-regulated anion channel subunit LRRC8A
KeywordsMEMBRANE PROTEIN / ion channel / leucine-rich repeat domain
Function / homology
Function and homology information


Miscellaneous transport and binding events / pre-B cell differentiation / volume-sensitive anion channel activity / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane transporter activity / cyclic-GMP-AMP transmembrane import across plasma membrane / monoatomic anion transmembrane transport / taurine transmembrane transport / protein hexamerization / cell volume homeostasis ...Miscellaneous transport and binding events / pre-B cell differentiation / volume-sensitive anion channel activity / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane transporter activity / cyclic-GMP-AMP transmembrane import across plasma membrane / monoatomic anion transmembrane transport / taurine transmembrane transport / protein hexamerization / cell volume homeostasis / monoatomic anion transport / response to osmotic stress / intracellular glucose homeostasis / monoatomic ion channel complex / positive regulation of myoblast differentiation / chloride transmembrane transport / positive regulation of insulin secretion / spermatogenesis / lysosomal membrane / cell surface / identical protein binding / plasma membrane
Similarity search - Function
LRRC8, pannexin-like TM region / Pannexin-like TM region of LRRC8 / : / : / Leucine-rich repeat region / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. ...LRRC8, pannexin-like TM region / Pannexin-like TM region of LRRC8 / : / : / Leucine-rich repeat region / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Volume-regulated anion channel subunit LRRC8A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsDeneka, D. / Sawicka, M. / Lam, A.K.M. / Paulino, C. / Dutzler, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Switzerland
CitationJournal: Nature / Year: 2018
Title: Structure of a volume-regulated anion channel of the LRRC8 family.
Authors: Dawid Deneka / Marta Sawicka / Andy K M Lam / Cristina Paulino / Raimund Dutzler /
Abstract: Volume-regulated anion channels are activated in response to hypotonic stress. These channels are composed of closely related paralogues of the leucine-rich repeat-containing protein 8 (LRRC8) family ...Volume-regulated anion channels are activated in response to hypotonic stress. These channels are composed of closely related paralogues of the leucine-rich repeat-containing protein 8 (LRRC8) family that co-assemble to form hexameric complexes. Here, using cryo-electron microscopy and X-ray crystallography, we determine the structure of a homomeric channel of the obligatory subunit LRRC8A. This protein conducts ions and has properties in common with endogenous heteromeric channels. Its modular structure consists of a transmembrane pore domain followed by a cytoplasmic leucine-rich repeat domain. The transmembrane domain, which is structurally related to connexin proteins, is wide towards the cytoplasm but constricted on the outside by a structural unit that acts as a selectivity filter. An excess of basic residues in the filter and throughout the pore attracts anions by electrostatic interaction. Our work reveals the previously unknown architecture of volume-regulated anion channels and their mechanism of selective anion conduction.
History
DepositionFeb 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Volume-regulated anion channel subunit LRRC8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4035
Polymers48,1551
Non-polymers2484
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint14 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.130, 140.130, 42.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Volume-regulated anion channel subunit LRRC8A / Leucine-rich repeat-containing protein 8A


Mass: 48155.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal domain of mouse LRRC8A / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lrrc8a, Lrrc8 / Plasmid: pcDNA3.1 / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human) / References: UniProt: Q80WG5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 22% PEG 3350, 0.2M Na/K tartrate, 0.1M Bis-Tris propane pH 8.5

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1, 2.05
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.051
ReflectionResolution: 1.8→40.452 Å / Num. obs: 44375 / % possible obs: 100 % / Redundancy: 20.2 % / Net I/σ(I): 27.05
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 19.8 % / Mean I/σ(I) obs: 2.27 / Num. unique obs: 6557 / CC1/2: 0.9 / Rrim(I) all: 1.58 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→40.452 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.35
RfactorNum. reflection% reflection
Rfree0.2082 1995 4.63 %
Rwork0.1792 --
obs0.1805 43134 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→40.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 16 337 3712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133497
X-RAY DIFFRACTIONf_angle_d1.274744
X-RAY DIFFRACTIONf_dihedral_angle_d17.9572184
X-RAY DIFFRACTIONf_chiral_restr0.07564
X-RAY DIFFRACTIONf_plane_restr0.009602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84510.33681190.31592430X-RAY DIFFRACTION81
1.8451-1.89490.29571250.29072600X-RAY DIFFRACTION87
1.8949-1.95070.30011380.24822791X-RAY DIFFRACTION93
1.9507-2.01370.28841430.2372995X-RAY DIFFRACTION100
2.0137-2.08560.24311430.20422969X-RAY DIFFRACTION100
2.0856-2.16910.21721500.19933002X-RAY DIFFRACTION100
2.1691-2.26780.23441490.18983013X-RAY DIFFRACTION100
2.2678-2.38740.22251420.18923000X-RAY DIFFRACTION100
2.3874-2.5370.24521450.18563023X-RAY DIFFRACTION100
2.537-2.73280.24871450.18283008X-RAY DIFFRACTION100
2.7328-3.00770.2021460.17723065X-RAY DIFFRACTION100
3.0077-3.44280.20711490.16843015X-RAY DIFFRACTION100
3.4428-4.33670.17291470.14393076X-RAY DIFFRACTION100
4.3367-40.46220.18581540.17833152X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.738 Å / Origin y: -45.7676 Å / Origin z: -1.9617 Å
111213212223313233
T0.218 Å20.0278 Å20.0119 Å2-0.2225 Å2-0.0183 Å2--0.2934 Å2
L2.9994 °21.6065 °2-0.3231 °2-1.6946 °2-0.2071 °2--0.611 °2
S0.0469 Å °0.0432 Å °0.4178 Å °0.0323 Å °0.0027 Å °0.1912 Å °-0.1378 Å °0.0207 Å °-0.0316 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more