[English] 日本語
Yorodumi
- EMDB-21434: Bestrophin-2 (BEST2) calcium-unbound state 1 (EGTA only) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21434
TitleBestrophin-2 (BEST2) calcium-unbound state 1 (EGTA only)
Map dataBestrophin-2 (BEST2) calcium-free state 1 (EGTA only)
Sample
  • Cell: bestrophin-2 (BEST2) calcium-free state 1 (EGTA only)
    • Protein or peptide: BestrophinCalcium-dependent chloride channel
  • Ligand: CHLORIDE IONChloride
  • Ligand: water
KeywordsChloride Channel / MEMBRANE PROTEIN
Function / homologyBestrophin / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel / Stimuli-sensing channels / chloride channel activity / chloride channel complex / plasma membrane / Bestrophin
Function and homology information
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.17 Å
AuthorsOwji AP / Zhao Q
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)F31EY030763 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY025290 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM127652 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM107462 United States
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structural and functional characterization of the bestrophin-2 anion channel.
Authors: Aaron P Owji / Qingqing Zhao / Changyi Ji / Alec Kittredge / Austin Hopiavuori / Ziao Fu / Nancy Ward / Oliver B Clarke / Yin Shen / Yu Zhang / Wayne A Hendrickson / Tingting Yang /
Abstract: The bestrophin family of calcium (Ca)-activated chloride (Cl) channels, which mediate the influx and efflux of monovalent anions in response to the levels of intracellular Ca, comprises four members ...The bestrophin family of calcium (Ca)-activated chloride (Cl) channels, which mediate the influx and efflux of monovalent anions in response to the levels of intracellular Ca, comprises four members in mammals (bestrophin 1-4). Here we report cryo-EM structures of bovine bestrophin-2 (bBest2) bound and unbound by Ca at 2.4- and 2.2-Å resolution, respectively. The bBest2 structure highlights four previously underappreciated pore-lining residues specifically conserved in Best2 but not in Best1, illustrating the differences between these paralogs. Structure-inspired electrophysiological analysis reveals that, although the channel is sensitive to Ca, it has substantial Ca-independent activity for Cl, reflecting the opening at the cytoplasmic restriction of the ion conducting pathway even when Ca is absent. Moreover, the ion selectivity of bBest2 is controlled by multiple residues, including those involved in gating.
History
DepositionFeb 21, 2020-
Header (metadata) releaseMar 11, 2020-
Map releaseApr 8, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6vx9
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vx9
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21434.png

Downloads & links

-
Map

FileDownload / File: emd_21434.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBestrophin-2 (BEST2) calcium-free state 1 (EGTA only)
Voxel sizeX=Y=Z: 0.35128 Å
Density
Contour LevelBy AUTHOR: 1.1 / Movie #1: 1.1
Minimum - Maximum-7.2480297 - 8.72892
Average (Standard dev.)0.000000000227142 (±0.53771484)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 118.03008 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.351279761904760.351279761904760.35127976190476
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z118.030118.030118.030
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ336336336
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS336336336
D min/max/mean-7.2488.7290.000

-
Supplemental data

-
Additional map: Additional map

Fileemd_21434_additional.map
AnnotationAdditional map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half-volume 1

Fileemd_21434_half_map_1.map
Annotationhalf-volume 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half-volume 2

Fileemd_21434_half_map_2.map
Annotationhalf-volume 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : bestrophin-2 (BEST2) calcium-free state 1 (EGTA only)

EntireName: bestrophin-2 (BEST2) calcium-free state 1 (EGTA only)
Components
  • Cell: bestrophin-2 (BEST2) calcium-free state 1 (EGTA only)
    • Protein or peptide: BestrophinCalcium-dependent chloride channel
  • Ligand: CHLORIDE IONChloride
  • Ligand: water

-
Supramolecule #1: bestrophin-2 (BEST2) calcium-free state 1 (EGTA only)

SupramoleculeName: bestrophin-2 (BEST2) calcium-free state 1 (EGTA only) / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (cattle)

-
Macromolecule #1: Bestrophin

MacromoleculeName: Bestrophin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 47.424754 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTVTYTARVA KARFGGFSKL LLLWRGSIYK LLWRELLCFL GLFMALSAAY RFVLTEEQKR YFEKLVLYCD RYASLIPVSF VLGFYVTLV VHRWWNQYLS MPLTDALMCV VVGTVHGHDE RGRLYRRTLM RYAGLSGVLI LRSVSTAVFK RFPTIDHVVE A GFMTREER ...String:
MTVTYTARVA KARFGGFSKL LLLWRGSIYK LLWRELLCFL GLFMALSAAY RFVLTEEQKR YFEKLVLYCD RYASLIPVSF VLGFYVTLV VHRWWNQYLS MPLTDALMCV VVGTVHGHDE RGRLYRRTLM RYAGLSGVLI LRSVSTAVFK RFPTIDHVVE A GFMTREER KKFENLNSSY NKYWVPCVWF CNLAAQARRE GRIRDNGAFK LLLEELNVFR SKCGMLFHYD WISVPLVYTQ VV TIAVYSY FLACLIGRQF LDPAQGYKDH DLDLCVPIFT LLQFFFYAGW LKVAEQLINP FGEDDDDFET NFLIDRCFQV SML AVDEMY DDLAMLEKDL YWDAAEARAP YTAATAFLMQ QPSFQGSTFD ITLAKEDMQF QRQDGLEAPL NEAHGDFLQR LLPV GTGMG TGGLL

UniProtKB: Bestrophin

-
Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

-
Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 455 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.8
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 69.67 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.13.2) / Number images used: 280524

+
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