[English] 日本語
Yorodumi
- EMDB-13417: Human voltage-gated potassium channel Kv3.1 (with Zn) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13417
TitleHuman voltage-gated potassium channel Kv3.1 (with Zn)
Map data
Sample
  • Complex: Homotetrameric complex of human Kv3.1
    • Protein or peptide: Potassium voltage-gated channel, Shaw-related subfamily, member 1Voltage-gated potassium channel
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
  • Ligand: ZINC ION
  • Ligand: POTASSIUM IONPotassium
Function / homology
Function and homology information


globus pallidus development / response to nerve growth factor / response to light intensity / response to potassium ion / response to auditory stimulus / response to fibroblast growth factor / delayed rectifier potassium channel activity / corpus callosum development / positive regulation of potassium ion transmembrane transport / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential ...globus pallidus development / response to nerve growth factor / response to light intensity / response to potassium ion / response to auditory stimulus / response to fibroblast growth factor / delayed rectifier potassium channel activity / corpus callosum development / positive regulation of potassium ion transmembrane transport / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / Voltage gated Potassium channels / optic nerve development / neuronal cell body membrane / response to amine / voltage-gated potassium channel activity / kinesin binding / calyx of Held / axolemma / voltage-gated potassium channel complex / axon terminus / potassium ion transmembrane transport / dendrite membrane / cerebellum development / protein tetramerization / protein homooligomerization / potassium ion transport / response to toxic substance / cellular response to xenobiotic stimulus / presynaptic membrane / postsynaptic membrane / transmembrane transporter binding / cell surface / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv3.1 / Potassium channel, voltage dependent, Kv3 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / 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 subfamily C member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChi G / Qian P / Castro-Hartmann P / Venkaya S / Singh NK / McKinley G / Mukhopadhyay SMM / Fernandez-Cid A / Marsden B / MacLean EM ...Chi G / Qian P / Castro-Hartmann P / Venkaya S / Singh NK / McKinley G / Mukhopadhyay SMM / Fernandez-Cid A / Marsden B / MacLean EM / Pike ACW / Sader K / Burgess-Brown NA / Duerr KL
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust106169/Z/14/Z United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM structure of the human Kv3.1 channel reveals gating control by the cytoplasmic T1 domain.
Authors: Gamma Chi / Qiansheng Liang / Akshay Sridhar / John B Cowgill / Kasim Sader / Mazdak Radjainia / Pu Qian / Pablo Castro-Hartmann / Shayla Venkaya / Nanki Kaur Singh / Gavin McKinley / ...Authors: Gamma Chi / Qiansheng Liang / Akshay Sridhar / John B Cowgill / Kasim Sader / Mazdak Radjainia / Pu Qian / Pablo Castro-Hartmann / Shayla Venkaya / Nanki Kaur Singh / Gavin McKinley / Alejandra Fernandez-Cid / Shubhashish M M Mukhopadhyay / Nicola A Burgess-Brown / Lucie Delemotte / Manuel Covarrubias / Katharina L Dürr /
Abstract: Kv3 channels have distinctive gating kinetics tailored for rapid repolarization in fast-spiking neurons. Malfunction of this process due to genetic variants in the KCNC1 gene causes severe epileptic ...Kv3 channels have distinctive gating kinetics tailored for rapid repolarization in fast-spiking neurons. Malfunction of this process due to genetic variants in the KCNC1 gene causes severe epileptic disorders, yet the structural determinants for the unusual gating properties remain elusive. Here, we present cryo-electron microscopy structures of the human Kv3.1a channel, revealing a unique arrangement of the cytoplasmic tetramerization domain T1 which facilitates interactions with C-terminal axonal targeting motif and key components of the gating machinery. Additional interactions between S1/S2 linker and turret domain strengthen the interface between voltage sensor and pore domain. Supported by molecular dynamics simulations, electrophysiological and mutational analyses, we identify several residues in the S4/S5 linker which influence the gating kinetics and an electrostatic interaction between acidic residues in α6 of T1 and R449 in the pore-flanking S6T helices. These findings provide insights into gating control and disease mechanisms and may guide strategies for the design of pharmaceutical drugs targeting Kv3 channels.
History
DepositionAug 17, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7phi
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13417.png

Downloads & links

-
Map

FileDownload / File: emd_13417.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.45 / Movie #1: 0.45
Minimum - Maximum-3.7020488 - 5.414608
Average (Standard dev.)0.012847147 (±0.09900135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-3.7025.4150.013

-
Supplemental data

-
Mask #1

Fileemd_13417_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_13417_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_13417_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Homotetrameric complex of human Kv3.1

EntireName: Homotetrameric complex of human Kv3.1
Components
  • Complex: Homotetrameric complex of human Kv3.1
    • Protein or peptide: Potassium voltage-gated channel, Shaw-related subfamily, member 1Voltage-gated potassium channel
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
  • Ligand: ZINC ION
  • Ligand: POTASSIUM IONPotassium

-
Supramolecule #1: Homotetrameric complex of human Kv3.1

SupramoleculeName: Homotetrameric complex of human Kv3.1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

-
Macromolecule #1: Potassium voltage-gated channel, Shaw-related subfamily, member 1

MacromoleculeName: Potassium voltage-gated channel, Shaw-related subfamily, member 1
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.850078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGQGDESERI VINVGGTRHQ THRSTLRTLP GTRLAWLAEP DAHSHFDYDP RADEFFFDRH PGVFAHILNY YRTGKLHCPA DVCGPLYEE ELAFWGIDET DVEPCCWMTY RQHRDAEEAL DSFGGAPLDN SADDADADGP GDSGDGEDEL EMTKRLALSD S PDGRPGGF ...String:
MGQGDESERI VINVGGTRHQ THRSTLRTLP GTRLAWLAEP DAHSHFDYDP RADEFFFDRH PGVFAHILNY YRTGKLHCPA DVCGPLYEE ELAFWGIDET DVEPCCWMTY RQHRDAEEAL DSFGGAPLDN SADDADADGP GDSGDGEDEL EMTKRLALSD S PDGRPGGF WRRWQPRIWA LFEDPYSSRY ARYVAFASLF FILVSITTFC LETHERFNPI VNKTEIENVR NGTQVRYYRE AE TEAFLTY IEGVCVVWFT FEFLMRVIFC PNKVEFIKNS LNIIDFVAIL PFYLEVGLSG LSSKAAKDVL GFLRVVRFVR ILR IFKLTR HFVGLRVLGH TLRASTNEFL LLIIFLALGV LIFATMIYYA ERIGAQPNDP SASEHTHFKN IPIGFWWAVV TMTT LGYGD MYPQTWSGML VGALCALAGV LTIAMPVPVI VNNFGMYYSL AMAKQKLPKK KKKHIPRPPQ LGSPNYCKSV VNSPH HSTQ SDTCPLAQEE ILEINRAGRK PLRGMSIAEN LYFQ

-
Macromolecule #2: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / type: ligand / ID: 2 / Number of copies: 8 / Formula: PCF
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PCF:
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / Dipalmitoylphosphatidylcholine

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #4: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS 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 K3 (6k x 4k) / Average electron dose: 47.59 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133488
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