[English] 日本語
Yorodumi
- PDB-6ci1: The Structure of Full-Length Kv Beta 2.1 Determined by Cryogenic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ci1
TitleThe Structure of Full-Length Kv Beta 2.1 Determined by Cryogenic Electron Microscopy
ComponentsVoltage-gated potassium channel subunit beta-2
KeywordsOXIDOREDUCTASE / Kv Channel / Regulator / Complex
Function / homology
Function and homology information


pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / Voltage gated Potassium channels / potassium channel complex / regulation of protein localization to cell surface / : / axon initial segment / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / juxtaparanode region of axon / myoblast differentiation ...pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / Voltage gated Potassium channels / potassium channel complex / regulation of protein localization to cell surface / : / axon initial segment / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / juxtaparanode region of axon / myoblast differentiation / regulation of potassium ion transmembrane transport / Neutrophil degranulation / neuromuscular process / voltage-gated potassium channel activity / potassium channel regulator activity / hematopoietic progenitor cell differentiation / voltage-gated potassium channel complex / axon terminus / postsynaptic density membrane / cytoplasmic side of plasma membrane / transmembrane transporter binding / cytoskeleton / neuron projection / postsynaptic density / axon / protein-containing complex binding / glutamatergic synapse / membrane / cytosol
Similarity search - Function
Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
Voltage-gated potassium channel subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsStagg, S.M. / Spear, J.M. / Mendez, J.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM086892 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108753 United States
CitationJournal: To Be Published
Title: The Structure of Full-Length Kv Beta 2.1 Determined by Cryogenic Electron Microscopy
Authors: Stagg, S.M. / Spear, J.M. / Mendez, J.H.
History
DepositionFeb 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7305
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Voltage-gated potassium channel subunit beta-2
B: Voltage-gated potassium channel subunit beta-2
C: Voltage-gated potassium channel subunit beta-2
D: Voltage-gated potassium channel subunit beta-2
E: Voltage-gated potassium channel subunit beta-2
F: Voltage-gated potassium channel subunit beta-2
G: Voltage-gated potassium channel subunit beta-2
H: Voltage-gated potassium channel subunit beta-2


Theoretical massNumber of molelcules
Total (without water)291,5288
Polymers291,5288
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Voltage-gated potassium channel subunit beta-2 / K(+) channel subunit beta-2 / Kv-beta-2 / Coordinate model: Cα atoms only


Mass: 36440.992 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnab2, Ckbeta2, Kcnb3 / Production host: Escherichia coli (E. coli)
References: UniProt: P62483, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Octamer of Kv Beta / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)

-
Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
13MDFFmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24809 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

+
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