[English] 日本語
Yorodumi
- EMDB-49336: C-terminal mVenues tagged Shaker T1 domain in C4 symmetry -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49336
TitleC-terminal mVenues tagged Shaker T1 domain in C4 symmetry
Map data
Sample
  • Cell: voltage-gated potassium channel Shaker
    • Protein or peptide: Potassium voltage-gated channel protein Shaker
Keywordsvoltage-gated potassium channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


mating behavior, sex discrimination / Phase 3 - rapid repolarisation / behavioral response to ether / Voltage gated Potassium channels / proboscis extension reflex / larval locomotory behavior / regulation of synaptic activity / courtship behavior / positive regulation of membrane potential / regulation of circadian sleep/wake cycle, sleep ...mating behavior, sex discrimination / Phase 3 - rapid repolarisation / behavioral response to ether / Voltage gated Potassium channels / proboscis extension reflex / larval locomotory behavior / regulation of synaptic activity / courtship behavior / positive regulation of membrane potential / regulation of circadian sleep/wake cycle, sleep / positive regulation of circadian sleep/wake cycle, sleep / detection of visible light / delayed rectifier potassium channel activity / sleep / cellular response to dopamine / axon extension / voltage-gated monoatomic cation channel activity / action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / protein homooligomerization / potassium ion transport / sensory perception of taste / perikaryon / learning or memory / neuron projection / membrane raft / membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium voltage-gated channel protein Shaker
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsTan X / Swartz KJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: Nature / Year: 2025
Title: Structural basis of fast N-type inactivation in K channels.
Authors: Xiao-Feng Tan / Ana I Fernández-Mariño / Yan Li / Tsg-Hui Chang / Kenton J Swartz /
Abstract: Action potentials are generated by opening of voltage-activated sodium (Na) and potassium (K) channels, which can rapidly inactivate to shape the nerve impulse and contribute to synaptic facilitation ...Action potentials are generated by opening of voltage-activated sodium (Na) and potassium (K) channels, which can rapidly inactivate to shape the nerve impulse and contribute to synaptic facilitation and short-term memory. The mechanism of fast inactivation was proposed to involve an intracellular domain that blocks the internal pore in both Na and K channels; however, recent studies in Na and K channels support a mechanism in which the internal pore closes during inactivation. Here we investigate the mechanism of fast inactivation in the Shaker K channel using cryo-electron microscopy, mass spectrometry and electrophysiology. We resolved structures of a fully inactivated state in which the non-polar end of the N terminus plugs the internal pore in an extended conformation. The N-terminal methionine is deleted, leaving an alanine that is acetylated and interacts with a pore-lining isoleucine residue where RNA editing regulates fast inactivation. Opening of the internal activation gate is required for fast inactivation because it enables the plug domain to block the pore and repositions gate residues to interact with and stabilize that domain. We also show that external K destabilizes the inactivated state by altering the conformation of the ion selectivity filter rather than by electrostatic repulsion. These findings establish the mechanism of fast inactivation in K channels, revealing how it is regulated by RNA editing and N-terminal acetylation, and providing a framework for understanding related mechanisms in other voltage-activated channels.
History
DepositionFeb 20, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49336.png

Downloads & links

-
Map

FileDownload / File: emd_49336.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.341
Minimum - Maximum-1.9020573 - 3.0586662
Average (Standard dev.)-0.0052590705 (±0.05163116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_49336_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_49336_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_49336_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : voltage-gated potassium channel Shaker

EntireName: voltage-gated potassium channel Shaker
Components
  • Cell: voltage-gated potassium channel Shaker
    • Protein or peptide: Potassium voltage-gated channel protein Shaker

-
Supramolecule #1: voltage-gated potassium channel Shaker

SupramoleculeName: voltage-gated potassium channel Shaker / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

-
Macromolecule #1: Potassium voltage-gated channel protein Shaker

MacromoleculeName: Potassium voltage-gated channel protein Shaker / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 75.459867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (ACE)AAVAGLYGL GEDRQHRKKQ QQQQQHQKEQ LEQKEEQKKI AERKLQLREQ QLQRNSLDGY GSLPKLSSQD EEGGAG HGF GGGPQHFEPI PHDHDFCERV VINVSGLRFE TQLRTLNQFP DTLLGDPARR LRYFDPLRNE YFFDRSRPSF DAILYYY QS GGRLRRPVNV ...String:
(ACE)AAVAGLYGL GEDRQHRKKQ QQQQQHQKEQ LEQKEEQKKI AERKLQLREQ QLQRNSLDGY GSLPKLSSQD EEGGAG HGF GGGPQHFEPI PHDHDFCERV VINVSGLRFE TQLRTLNQFP DTLLGDPARR LRYFDPLRNE YFFDRSRPSF DAILYYY QS GGRLRRPVNV PLDVFSEEIK FYELGDQAIN KFREDEGFIK EEERPLPDNE KQRKVWLLFE YPESSQAARV VAIISVFV I LLSIVIFCLE TLPEFKHYKV FNTTTNGTKI EEDEVPDITD PFFLIETLCI IWFTFELTVR FLACPNKLNF CRDVMNVID IIAIIPYFIT LATVVAEEED TLNLPKAPVS PQDKSSNQAM SLAILRVIRL VRVFRIFKLS RHSKGLQILG RTLKASMREL GLLIFFLFI GVVLFSSAVY FAEAGSENSF FKSIPDAFWW AVVTMTTVGY GDMTPVGVWG KIVGSLCAIA GVLTIALPVP V IVSNFNYF YHRETDQEEM QSQNFNHVTS CPYLPGTLVG QHMKKSSLSE SSSDMMDLDD GVESTPGLTE THPGRSAVAP FL GAQQQQQ QPVASSLSMS IDKQLQHPLQ QLTQTQLYQQ QQQQQQQQQN GFKQQQQQTQ QQLQQQQSHT INASAAAATS GSG SSGLTM RHNNALAVSI ETDVGSGGGS ENLYFQ

UniProtKB: Potassium voltage-gated channel protein Shaker

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
46.0 mMNaClsodium chloride
4.0 mMKClpotassium chloride
20.0 mMTris-Cltris(hydroxymethyl)aminomethane hydrochloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 325375
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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