[English] 日本語
Yorodumi
- EMDB-49554: R162Q mutant of inwardly rectifying potassium channel Kir7.1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49554
TitleR162Q mutant of inwardly rectifying potassium channel Kir7.1
Map datainwardly rectifying potassium channel Kir7.1 R162Q mutant in MNG micelle
Sample
  • Complex: potassium channel tetramer of four identical subunits of inwardly rectifying potassium channel Kir7.1
    • Protein or peptide: Inward rectifier potassium channel 13
  • Ligand: POTASSIUM ION
Keywordsinwardly rectifying potassium channel Kir7.1 / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of monoatomic ion transmembrane transport / inward rectifier potassium channel activity / potassium ion import across plasma membrane / monoatomic ion channel complex / potassium ion transport / plasma membrane
Similarity search - Function
Inward rectifier potassium channel 13 / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / Immunoglobulin E-set
Similarity search - Domain/homology
Inward rectifier potassium channel 13
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsPeisley A / Cone R
Funding support United States, 1 items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: To Be Published
Title: ML418 Binds in the Pore of the Inward Rectifier Kir7.1 and Inhibits the Channel In Vivo to Reduce Food Intake and Body Weight
Authors: Peisley A / Cone R
History
DepositionMar 4, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49554.png

Downloads & links

-
Map

FileDownload / File: emd_49554.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationinwardly rectifying potassium channel Kir7.1 R162Q mutant in MNG micelle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-1.2142447 - 2.113437
Average (Standard dev.)0.00005491425 (±0.05230785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.04 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: inwardly rectifying potassium channel Kir7.1 R162Q mutant in...

Fileemd_49554_half_map_1.map
Annotationinwardly rectifying potassium channel Kir7.1 R162Q mutant in MNG micelle
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: inwardly rectifying potassium channel Kir7.1 R162Q mutant in...

Fileemd_49554_half_map_2.map
Annotationinwardly rectifying potassium channel Kir7.1 R162Q mutant in MNG micelle
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : potassium channel tetramer of four identical subunits of inwardly...

EntireName: potassium channel tetramer of four identical subunits of inwardly rectifying potassium channel Kir7.1
Components
  • Complex: potassium channel tetramer of four identical subunits of inwardly rectifying potassium channel Kir7.1
    • Protein or peptide: Inward rectifier potassium channel 13
  • Ligand: POTASSIUM ION

-
Supramolecule #1: potassium channel tetramer of four identical subunits of inwardly...

SupramoleculeName: potassium channel tetramer of four identical subunits of inwardly rectifying potassium channel Kir7.1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Inward rectifier potassium channel 13

MacromoleculeName: Inward rectifier potassium channel 13 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.49627 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SDSSNCKVIA PLLSQRYRRM VTKDGHSTLQ MDGAQRGLAY LRDAWGILMD MRWRWMMLVF SASFVVHWLV FAVLWYVLAE MNGDLELDH DAPPENHTIC VKYITSFTAA FSFSLETQLT IGYGTMFPSG DCPSAIALLA IQMLLGLMLE AFITGAFVAK I AQPKNRAF ...String:
SDSSNCKVIA PLLSQRYRRM VTKDGHSTLQ MDGAQRGLAY LRDAWGILMD MRWRWMMLVF SASFVVHWLV FAVLWYVLAE MNGDLELDH DAPPENHTIC VKYITSFTAA FSFSLETQLT IGYGTMFPSG DCPSAIALLA IQMLLGLMLE AFITGAFVAK I AQPKNRAF SIRFTDTAVV AHMDGKPNLI FQVANTRPSP LTSVRVSAVL YQERENGKLY QTSVDFHLDG ISSDECPFFI FP LTYYHSI TPSSPLATLL QHENPSHFEL VVFLSAMQEG TGEICQRRTS YLPSEIMLHH CFASLLTRGS KGEYQIKMEN FDK TVPEFP TPLVSKSPNR TDLDIHINGQ SIDNFQISET GLTE

UniProtKB: Inward rectifier potassium channel 13

-
Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration8 mg/mL
BufferpH: 7.4
GridMaterial: GOLD
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75909
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9nms:
R162Q mutant of inwardly rectifying potassium channel Kir7.1

+
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