[English] 日本語
Yorodumi
- PDB-9ezc: Structure of the extracellular subdomain of a homomeric LRRC8C tr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ezc
TitleStructure of the extracellular subdomain of a homomeric LRRC8C truncation disease mutant
ComponentsVolume-regulated anion channel subunit LRRC8C
KeywordsMEMBRANE PROTEIN / Anion channel / Volume regulation / disease mutation
Function / homology
Function and homology information


Miscellaneous transport and binding events / volume-sensitive anion channel activity / taurine transmembrane transport / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane import across plasma membrane / monoatomic anion transmembrane transport / cellular response to osmotic stress / protein hexamerization / monoatomic ion channel complex / fat cell differentiation ...Miscellaneous transport and binding events / volume-sensitive anion channel activity / taurine transmembrane transport / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane import across plasma membrane / monoatomic anion transmembrane transport / cellular response to osmotic stress / protein hexamerization / monoatomic ion channel complex / fat cell differentiation / endoplasmic reticulum membrane / membrane / plasma membrane / cytoplasm
Similarity search - Function
LRRC8, pannexin-like TM region / Pannexin-like TM region of LRRC8 / : / 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 LRRC8C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsRutz, S. / Quinodoz, M. / Peter, V. / Garavelli, L. / Innes, M.A. / Kellenberger, S. / Peng, Z. / Barone, A. / Campos-Xavier, B. / Unger, S. ...Rutz, S. / Quinodoz, M. / Peter, V. / Garavelli, L. / Innes, M.A. / Kellenberger, S. / Peng, Z. / Barone, A. / Campos-Xavier, B. / Unger, S. / Rivolta, C. / Dutzler, R. / Superti-Furga, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationNo. 310030_204373 Switzerland
CitationJournal: To Be Published
Title: Genetic activation of Volume-Regulated Anion Channels cause a multisystem disorder
Authors: Rutz, S. / Quinodoz, M. / Peter, V. / Garavelli, L. / Innes, M.A. / Kellenberger, S. / Peng, Z. / Barone, A. / Campos-Xavier, B. / Unger, S. / Rivolta, C. / Dutzler, R. / Superti-Furga, A.
History
DepositionApr 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Volume-regulated anion channel subunit LRRC8C
B: Volume-regulated anion channel subunit LRRC8C
C: Volume-regulated anion channel subunit LRRC8C
D: Volume-regulated anion channel subunit LRRC8C
E: Volume-regulated anion channel subunit LRRC8C
F: Volume-regulated anion channel subunit LRRC8C
G: Volume-regulated anion channel subunit LRRC8C


Theoretical massNumber of molelcules
Total (without water)334,0407
Polymers334,0407
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Volume-regulated anion channel subunit LRRC8C / Factor for adipocyte differentiation 158 / Leucine-rich repeat-containing protein 8C


Mass: 47719.941 Da / Num. of mol.: 7 / Mutation: Leu400IlefsTer8
Source method: isolated from a genetically manipulated source
Details: The compound only shows the extracellular subdomain (ESD) of the channel
Source: (gene. exp.) Homo sapiens (human) / Gene: LRRC8C, AD158, FAD158 / Production host: Homo sapiens (human) / References: UniProt: Q8TDW0
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Homomeric LRRC8C truncation disease mutant / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224687 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 50.47 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325894
ELECTRON MICROSCOPYf_angle_d0.87347945
ELECTRON MICROSCOPYf_chiral_restr0.0519875
ELECTRON MICROSCOPYf_plane_restr0.0042973
ELECTRON MICROSCOPYf_dihedral_angle_d4.9954749

+
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