[English] 日本語
Yorodumi
- EMDB-2710: E. coli potassium channel 3D structure by electron crystallography -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2710
TitleE. coli potassium channel 3D structure by electron crystallography
Map dataThe four-fold symmetrized map was generated by averaging the 3D maps rotated at 0degree, 90degree, 180degree, and 270degree around the c-axis. The structure of MlotiK1 (PDB ID: 3BEH) was docked as a similar protein to Kch into the symmetrized map using Chimera.
Sample
  • Sample: voltage-gated potassium channel, four-fold symmetrized map
  • Protein or peptide: Kch
KeywordsPotassium channel / 6TM / RCK
Function / homology
Function and homology information


transport / potassium channel activity / membrane => GO:0016020 / monoatomic ion transport / potassium ion transmembrane transport / potassium ion transport / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / : / Regulator of K+ conductance, N-terminal / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Voltage-gated potassium channel / Potassium channel domain / Ion channel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Voltage-gated potassium channel Kch
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodelectron crystallography / cryo EM / negative staining / Resolution: 10.0 Å
AuthorsKuang Q / Purhonen P / Jegerschold C / Koeck PJB / Hebert H
CitationJournal: Structure / Year: 2015
Title: Free RCK arrangement in Kch, a putative escherichia coli potassium channel, as suggested by electron crystallography.
Authors: Qie Kuang / Pasi Purhonen / Caroline Jegerschöld / Philip J B Koeck / Hans Hebert /
Abstract: The ligand-gated potassium channels are stimulated by various kinds of messengers. Previous studies showed that ligand-gated potassium channels containing RCK domains (the regulator of the ...The ligand-gated potassium channels are stimulated by various kinds of messengers. Previous studies showed that ligand-gated potassium channels containing RCK domains (the regulator of the conductance of potassium ion) form a dimer of tetramer structure through the RCK octameric gating ring in the presence of detergent. Here, we have analyzed the structure of Kch, a channel of this type from Escherichia coli, in a lipid environment using electron crystallography. By combining information from the 3D map of the transmembrane part of the protein and docking of an atomic model of a potassium channel, we conclude that the RCK domains face the solution and that an RCK octameric gating ring arrangement does not form under our crystallization condition. Our findings may be applied to other potassium channels that have an RCK gating ring arrangement.
History
DepositionJul 11, 2014-
Header (metadata) releaseJul 23, 2014-
Map releaseJan 21, 2015-
UpdateJan 21, 2015-
Current statusJan 21, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2710.jpg

Downloads & links

-
Map

FileDownload / File: emd_2710.map.gz / Format: CCP4 / Size: 115.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe four-fold symmetrized map was generated by averaging the 3D maps rotated at 0degree, 90degree, 180degree, and 270degree around the c-axis. The structure of MlotiK1 (PDB ID: 3BEH) was docked as a similar protein to Kch into the symmetrized map using Chimera.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
3.17 Å/pix.
x 26 pix.
= 82.501 Å		3.25 Å/pix.
x 44 pix.
= 84.5 Å		3.17 Å/pix.
x 26 pix.
= 139.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 3.25 Å / Y: 3.1731 Å / Z: 3.1731 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.13750449 - 0.19824362
Average (Standard dev.)-0.00201802 (±0.03603045)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions442626
Spacing262644
CellA: 84.5 Å / B: 82.5006 Å / C: 139.6164 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.253.17311538461543.1730909090909
M x/y/z262644
origin x/y/z0.0000.0000.000
length x/y/z84.50082.501139.616
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ442626
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS264426
D min/max/mean-0.1380.198-0.002

-
Supplemental data

-
Sample components

-
Entire : voltage-gated potassium channel, four-fold symmetrized map

EntireName: voltage-gated potassium channel, four-fold symmetrized map
Components
  • Sample: voltage-gated potassium channel, four-fold symmetrized map
  • Protein or peptide: Kch

-
Supramolecule #1000: voltage-gated potassium channel, four-fold symmetrized map

SupramoleculeName: voltage-gated potassium channel, four-fold symmetrized map
type: sample / ID: 1000 / Oligomeric state: tetramers / Number unique components: 1

-
Macromolecule #1: Kch

MacromoleculeName: Kch / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Oligomeric state: tetramer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12 / Location in cell: inner membrane
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: c43 / Recombinant plasmid: pSP19T7LT
SequenceUniProtKB: Voltage-gated potassium channel Kch
GO: transport, monoatomic ion transport, potassium ion transport, plasma membrane, potassium ion transmembrane transport, membrane, membrane => GO:0016020
InterPro: INTERPRO: IPR003091, Regulator of K+ conductance, N-terminal, Voltage-gated potassium channel

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingelectron crystallography
Aggregation state2D array

-
Sample preparation

Concentration0.7 mg/mL
BufferDetails: 25 mM Na-acetate at pH 7, 20% glycerol, 100 mM KCl, 0.1 mM EDTA, 1 mM reduced glutathione, 50 mM MgCl2, with or without 5% (w/v) glycine
StainingType: NEGATIVE / Details: Embedded in trehalose
GridDetails: Copper grid with carbon
VitrificationCryogen name: NITROGEN / Chamber humidity: 20 % / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER / Details: Manual freezing
DetailsCrystal grown by dialysis away the detergent
Crystal formationDetails: Crystal grown by dialysis away the detergent

-
Electron microscopy

MicroscopeJEOL 2100F
TemperatureAverage: 95 K
DateMar 1, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 33 / Average electron dose: 12 e/Å2 / Bits/pixel: 16
Tilt angle min0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 45 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 45 °

-
Image processing

DetailsThe four-fold symmetrized map was generated using ccp4. B = -500 is used to boost the fall-off of the amplitudes at intermediate and high resolution in the map.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: OTHER / Software - Name: MRC
Crystal parametersUnit cell - A: 143 Å / Unit cell - B: 82 Å / Unit cell - γ: 90 ° / Plane group: C 1 2
CTF correctionDetails: Each image

-
Atomic model buiding 1

Initial modelPDB ID:

3beh

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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