[English] 日本語
Yorodumi
- EMDB-24613: CLC-ec1 at pH 4.5 100 mM NaGluconate Swap -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24613
TitleCLC-ec1 at pH 4.5 100 mM NaGluconate Swap
Map dataCLC-ec1 pH 4.5 0 mM Cl Swap
Sample
  • Complex: Structure of ecCLC at pH 4.5 in 100mM NaGluconate
    • Protein or peptide: H(+)/Cl(-) exchange transporter ClcA
KeywordsCLC / chloride transporter / MEMBRANE PROTEIN
Function / homologyChloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / voltage-gated chloride channel activity / antiporter activity / plasma membrane / H(+)/Cl(-) exchange transporter ClcA
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsFortea E / Boudker O
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structural basis of common gate activation in CLC transporters
Authors: Fortea E / Lee S / Argyros Y / Chadda R / Ciftci D / Huysmans G / Robertson JL / Boudker O / Accardi A
History
DepositionAug 3, 2021-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_24613.png

Downloads & links

-
Map

FileDownload / File: emd_24613.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCLC-ec1 pH 4.5 0 mM Cl Swap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 196 pix.
= 205.408 Å		1.05 Å/pix.
x 196 pix.
= 205.408 Å		1.05 Å/pix.
x 196 pix.
= 205.408 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.907085 - 1.367745
Average (Standard dev.)0.003098388 (±0.035618294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 205.40799 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Structure of ecCLC at pH 4.5 in 100mM NaGluconate

EntireName: Structure of ecCLC at pH 4.5 in 100mM NaGluconate
Components
  • Complex: Structure of ecCLC at pH 4.5 in 100mM NaGluconate
    • Protein or peptide: H(+)/Cl(-) exchange transporter ClcA

-
Supramolecule #1: Structure of ecCLC at pH 4.5 in 100mM NaGluconate

SupramoleculeName: Structure of ecCLC at pH 4.5 in 100mM NaGluconate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 100 kDa/nm

-
Macromolecule #1: H(+)/Cl(-) exchange transporter ClcA

MacromoleculeName: H(+)/Cl(-) exchange transporter ClcA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 50.390402 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKTDTPSLET PQAARLRRRQ LIRQLLERDK TPLAILFMAA VVGTLVGLAA VAFDKGVAWL QNQRMGALVH TADNYPLLLT VAFLCSAVL AMFGYFLVRK YAPEAGGSGI PEIEGALEDQ RPVRWWRVLP VKFFGGLGTL GGGMVLGREG PTVQIGGNIG R MVLDIFRL ...String:
MKTDTPSLET PQAARLRRRQ LIRQLLERDK TPLAILFMAA VVGTLVGLAA VAFDKGVAWL QNQRMGALVH TADNYPLLLT VAFLCSAVL AMFGYFLVRK YAPEAGGSGI PEIEGALEDQ RPVRWWRVLP VKFFGGLGTL GGGMVLGREG PTVQIGGNIG R MVLDIFRL KGDEARHTLL ATGAAAGLAA AFNAPLAGIL FIIEEMRPQF RYTLISIKAV FIGVIMSTIM YRIFNHEVAL ID VGKLSDA PLNTLWLYLI LGIIFGIFGP IFNKWVLGMQ DLLHRVHGGN ITKWVLMGGA IGGLCGLLGF VAPATSGGGF NLI PIATAG NFSMGMLVFI FVARVITTLL CFSSGAPGGI FAPMLALGTV LGTAFGMVAV ELFPQYHLEA GTFAIAGMGA LLAA SIRAP LTGIILVLEM TDNYQLILPM IITGLGATLL AQFTGGKPLY SAILARTLAK QEAEQLARSK AASASENT

UniProtKB: H(+)/Cl(-) exchange transporter ClcA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.7 mg/mL
BufferpH: 4.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294.15 K

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.08 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115851
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

+
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