[English] 日本語
Yorodumi
- EMDB-55892: Unknown entry -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55892
TitleCryo-EM structure of the inward rectifying potassium channel 7.1 (Kir7.1) in complex with PIP2
Map data
Sample
  • Complex: Tetrameric assembly of human inward rectifying potassium channel 7.1
    • Protein or peptide: Inward rectifier potassium channel 13
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
  • Ligand: POTASSIUM ION
Keywordspotassium ion channel / active conformation / human membrane protein / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsO'Malley N / Faust B / Nasrallah C / Wallace BA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of human Kir7.1 reveals the molecular basis of Snowflake Vitreoretinal Degeneration
Authors: O'Malley N / Nasrallah C / Faust B / Wallace B
History
DepositionNov 28, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55892.png

Downloads & links

-
Map

FileReleased
Voxel sizeX=Y=Z: 0.65 Å
Density
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-1.8599255 - 2.5311782
Average (Standard dev.)0.00053959334 (±0.03517521)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 286.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Tetrameric assembly of human inward rectifying potassium channel 7.1

EntireName: Tetrameric assembly of human inward rectifying potassium channel 7.1
Components
  • Complex: Tetrameric assembly of human inward rectifying potassium channel 7.1
    • Protein or peptide: Inward rectifier potassium channel 13
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
  • Ligand: POTASSIUM ION

-
Supramolecule #1: Tetrameric assembly of human inward rectifying potassium channel 7.1

SupramoleculeName: Tetrameric assembly of human inward rectifying potassium channel 7.1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human) / Location in cell: Plasma membrane

-
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: 42.377262 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKGS MDSSNCKVIA PLLSQRYRRM VTKDGHSTLQ MDGAQRGLAY LRDAWGILMD MRWRWMMLVF SASFVVHWLV FAVLWYVLA EMNGDLELDH DAPPENHTIC VKYITSFTAA FSFSLETQLT IGYGTMFPSG DCPSAIALLA IQMLLGLMLE A FITGAFVA ...String:
DYKDDDDKGS MDSSNCKVIA PLLSQRYRRM VTKDGHSTLQ MDGAQRGLAY LRDAWGILMD MRWRWMMLVF SASFVVHWLV FAVLWYVLA EMNGDLELDH DAPPENHTIC VKYITSFTAA FSFSLETQLT IGYGTMFPSG DCPSAIALLA IQMLLGLMLE A FITGAFVA KIARPKNRAF SIRFTDTAVV AHMDGKPNLI FQVANTRPSP LTSVRVSAVL YQERENGKLY QTSVDFHLDG IS SDECPFF IFPLTYYHSI TPSSPLATLL QHENPSHFEL VVFLSAMQEG TGEICQRRTS YLPSEIMLHH CFASLLTRGS KGE YQIKME NFDKTVPEFP TPLVSKSPNR TDLDIHINGQ SIDNFQISET GLTEENLYF

UniProtKB: Inward rectifier potassium channel 13

-
Macromolecule #2: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
type: ligand / ID: 2 / Number of copies: 4 / Formula: PIO
Molecular weightTheoretical: 746.566 Da
Chemical component information

ChemComp-PIO:
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

-
Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration6 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 22098 / Average electron dose: 31.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 8821241
CTF correctionSoftware - Name: cryoSPARC (ver. v3.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 556510
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.2)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.2)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9tg6:
Cryo-EM structure of the inward rectifying potassium channel 7.1 (Kir7.1) in complex with PIP2

+
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