[English] 日本語
Yorodumi
- EMDB-68402: Cryo-EM structure of AtSLAH3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-68402
TitleCryo-EM structure of AtSLAH3
Map data
Sample
  • Complex: SLAH3
    • Protein or peptide: S-type anion channel SLAH3
Keywordshomotrimer / membrane protein / plant protein / transport protein
Function / homology
Function and homology information


voltage-gated monoatomic anion channel activity / intracellular monoatomic ion homeostasis / response to water deprivation / chloride transport / response to salt stress / plasma membrane
Similarity search - Function
S-type anion channel / Transporter protein SLAC1/Mae1/ Ssu1/TehA / Voltage-dependent anion channel superfamily / Voltage-dependent anion channel
Similarity search - Domain/homology
S-type anion channel SLAH3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsShuai G / Xia Y / Yuqin W
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22477098 China
CitationJournal: To Be Published
Title: Cryo-EM structure of AtSLAH3
Authors: Shuai G / Xia Y / Yuqin W
History
DepositionJan 14, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_68402.png

Downloads & links

-
Map

FileDownload / File: emd_68402.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 263.68 Å		0.82 Å/pix.
x 320 pix.
= 263.68 Å		0.82 Å/pix.
x 320 pix.
= 263.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.3986051 - 1.9093406
Average (Standard dev.)-0.0010274322 (±0.04170867)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_68402_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_68402_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SLAH3

EntireName: SLAH3
Components
  • Complex: SLAH3
    • Protein or peptide: S-type anion channel SLAH3

-
Supramolecule #1: SLAH3

SupramoleculeName: SLAH3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

-
Macromolecule #1: S-type anion channel SLAH3

MacromoleculeName: S-type anion channel SLAH3 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 72.421453 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEKPNYVIQ VEEELPTLLR KATTEEMVGF DNYKENGHPF PHSISRFHPS HASTTTLNGQ ETSRSIDTME AHHHNYNETT PWTHQRKPS ISMPTSPNVL MISDPTTSLS SENHKNSGST GKSVKFLSQP MTKVSSLYIE SGNGDDDRRQ SHDNHHHHLH R QHQSGHHQ ...String:
MEEKPNYVIQ VEEELPTLLR KATTEEMVGF DNYKENGHPF PHSISRFHPS HASTTTLNGQ ETSRSIDTME AHHHNYNETT PWTHQRKPS ISMPTSPNVL MISDPTTSLS SENHKNSGST GKSVKFLSQP MTKVSSLYIE SGNGDDDRRQ SHDNHHHHLH R QHQSGHHQ NQNQAANKLK DNRYNSFKTW SGKLERQFTR KPASVEPEAP NRNNQNLNTN EAMPVDRYYD ALEGPELETL RP QEEIVLP NDKKWPFLLR YPISTFGMCL GVSSQAIMWK TLATAEPTKF LHVPLWINQG LWFISVALIL TIATIYLLKI ILF FEAVRR EYYHPIRINF FFAPFISLLF LALGVPPSII TDLPHFLWYL LMFPFICLEL KIYGQWMSGG QRRLSRVANP TNHL SVVGN FVGALLGASM GLREGPIFFY AVGMAHYLVL FVTLYQRLPT NETLPKDLHP VFFLFVAAPS VASMAWAKVT GSFDY GSKV CYFIAIFLYF SLAVRINFFR GIKFSLSWWA YTFPMTGAAI ATIRYATVVK STMTQIMCVV LCAIATLVVF ALLVTT IIH AFVLRDLFPN DLAIAISNRP RPKQNSQHRW LDQLRNVSSE NIENYLKFTD SDSSQSNDVE ACNGKTQESD SS

UniProtKB: S-type anion channel SLAH3

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 110526
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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