[English] 日本語
Yorodumi
- EMDB-37855: SKOR D312N L271P double mutation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37855
TitleSKOR D312N L271P double mutation
Map data
Sample
  • Complex: SKOR double mutation tetramer
    • Protein or peptide: Potassium channel SKOR
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
KeywordsPotassium transport / Cryo-EM / ion channel / METAL TRANSPORT
Function / homology
Function and homology information


potassium ion homeostasis / outward rectifier potassium channel activity / monoatomic ion channel complex / potassium ion transport
Similarity search - Function
Potassium channel KAT/AKT / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily ...Potassium channel KAT/AKT / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium channel SKOR
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGao X / Sun T / Lu Y / Jia Y / Xu X / Zhang Y / Fu P / Yang G
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171188 China
CitationJournal: Plant Commun / Year: 2024
Title: Structural changes in the conversion of an Arabidopsis outward-rectifying K channel into an inward-rectifying channel.
Authors: Xudong Gao / Xia Xu / Tengfei Sun / Yuhan Lu / Yutian Jia / Jiaqi Zhou / Peng Fu / Yanming Zhang / Guanghui Yang /
History
DepositionOct 20, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37855.png

Downloads & links

-
Map

FileDownload / File: emd_37855.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 280 pix.
= 291.2 Å		1.04 Å/pix.
x 280 pix.
= 291.2 Å		1.04 Å/pix.
x 280 pix.
= 291.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.184
Minimum - Maximum-1.079451 - 1.7954745
Average (Standard dev.)0.0020950572 (±0.032087144)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 291.19998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_37855_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37855_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SKOR double mutation tetramer

EntireName: SKOR double mutation tetramer
Components
  • Complex: SKOR double mutation tetramer
    • Protein or peptide: Potassium channel SKOR
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

-
Supramolecule #1: SKOR double mutation tetramer

SupramoleculeName: SKOR double mutation tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

-
Macromolecule #1: Potassium channel SKOR

MacromoleculeName: Potassium channel SKOR / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 95.260367 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDDDDKH MGGSSGGGVS YRSGGESDVE LEDYEVDDFR DGIVESRGNR FNPLTNFLGL DFAGGSGGKF TVINGIRDIS RGSIVHPDN RWYKAWTMFI LIWALYSSFF TPLEFGFFRG LPENLFILDI AGQIAFLVDI VLTFFVAYRD SRTYRMIYKR S SIALRYLK ...String:
MDYKDDDDKH MGGSSGGGVS YRSGGESDVE LEDYEVDDFR DGIVESRGNR FNPLTNFLGL DFAGGSGGKF TVINGIRDIS RGSIVHPDN RWYKAWTMFI LIWALYSSFF TPLEFGFFRG LPENLFILDI AGQIAFLVDI VLTFFVAYRD SRTYRMIYKR S SIALRYLK STFIIDLLAC MPWDIIYKAA GEKEEVRYLL LIRLYRVHRV ILFFHKMEKD IRINYLFTRI VKLIFVELYC TH TAACIFY YLATTLPASQ EGYTWIGSLK LGDYSYSKFR EIDPWTRYTT SMYFAVVTMA TVGYGDIHAV NMREMIFAMV YIS FNMILG AYLIGNMTAL IVKGSKTERF RDKMADIMRY MNRNKLGRNI RGQITGHLRL QYESSYTEAA VLQDIPVSIR AKIA QTLYL PYIEKVPLFR GCSSEFINQI VIRLHEEFFL PGEVIMEQGS VVDQLYFVCH GVLEEIGITK DGSEEIVAVL QPDHS FGEI SILCNIPQPY TVRVAELCRI LRLDKQSFMN ILEIFFHDGR RILNNLLEGK ESNVRIKQLE SDITFHISKQ EAELAL KLN SAAFYGDLYQ LKSLIRAGGD PNKTDYDGRS PLHLAASRGY EDITLYLIQE SVDVNIKDKL GSTPLLEAIK NGNDRVA AL LVKEGATLNI ENAGTFLCTV VAKGDSDFLK RLLSNGIDPN SKDYDHRTPL HVAASEGFYV LAIQLVEASA NVLAKDRW G NTPLDEALGC GNKMLIKLLE DAKNSQISSF PSGSKEPKDK VYKKKCTVYF SHPGDSKEKR RRGIVLWVPR SIEELIRTA KEQLNVPEAS CVLSEDEAKI IDVDLISDGQ KLYLAVET

UniProtKB: Potassium channel SKOR

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

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 14 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN 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: DIFFRACTION / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97040
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