[English] 日本語
Yorodumi
- EMDB-9361: Structure of chicken Otop3 in nanodiscs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9361
TitleStructure of chicken Otop3 in nanodiscs
Map dataStructure of chOtop3 in lipidic nanodiscs
Sample
  • Complex: Zebrafish Otopetrin1 in lipidic nanodiscs
    • Protein or peptide: Otopetrin3
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsProton channel / Otopetrin / MEMBRANE PROTEIN
Biological speciesDanio rerio (zebrafish) / Gallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsSaotome K / Lee WH
Funding support United States, 2 items
OrganizationGrant numberCountry
Other private United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)NIDCD013741 United States
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Structures of the otopetrin proton channels Otop1 and Otop3.
Authors: Kei Saotome / Bochuan Teng / Che Chun Alex Tsui / Wen-Hsin Lee / Yu-Hsiang Tu / Joshua P Kaplan / Mark S P Sansom / Emily R Liman / Andrew B Ward /
Abstract: Otopetrins (Otop1-Otop3) comprise one of two known eukaryotic proton-selective channel families. Otop1 is required for otoconia formation and a candidate mammalian sour taste receptor. Here we report ...Otopetrins (Otop1-Otop3) comprise one of two known eukaryotic proton-selective channel families. Otop1 is required for otoconia formation and a candidate mammalian sour taste receptor. Here we report cryo-EM structures of zebrafish Otop1 and chicken Otop3 in lipid nanodiscs. The structures reveal a dimeric architecture, with each subunit forming 12 transmembrane helices divided into structurally similar amino (N) and carboxy (C) domains. Cholesterol-like molecules occupy various sites in Otop1 and Otop3 and occlude a central tunnel. In molecular dynamics simulations, hydrophilic vestibules formed by the N and C domains and in the intrasubunit interface between N and C domains form conduits for water entry into the membrane core, suggesting three potential proton conduction pathways. By mutagenesis, we tested the roles of charged residues in each putative permeation pathway. Our results provide a structural basis for understanding selective proton permeation and gating of this conserved family of proton channels.
History
DepositionDec 18, 2018-
Header (metadata) releaseFeb 20, 2019-
Map releaseJun 5, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6nf6
  • Surface level: 5.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9361.png

Downloads & links

-
Map

FileDownload / File: emd_9361.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of chOtop3 in lipidic nanodiscs
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 5.5 / Movie #1: 5.5
Minimum - Maximum-19.310072000000002 - 26.482925000000002
Average (Standard dev.)0.000000000010935 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 206.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z206.000206.000206.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-19.31026.4830.000

-
Supplemental data

-
Sample components

-
Entire : Zebrafish Otopetrin1 in lipidic nanodiscs

EntireName: Zebrafish Otopetrin1 in lipidic nanodiscs
Components
  • Complex: Zebrafish Otopetrin1 in lipidic nanodiscs
    • Protein or peptide: Otopetrin3
  • Ligand: CHOLESTEROL HEMISUCCINATE

-
Supramolecule #1: Zebrafish Otopetrin1 in lipidic nanodiscs

SupramoleculeName: Zebrafish Otopetrin1 in lipidic nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 65853 kDa/nm

-
Macromolecule #1: Otopetrin3

MacromoleculeName: Otopetrin3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 63.744496 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPAGNKASKQ KFCHHCNSRS ASAPPGTSTI HYEKSWLYRH CSLQQRDRQA QKSGQLFSGL LALNVVFLGS AFISSMIFNH VAITLADVW ILLSILKVLC LCWIIYYLLG TSRQPHAVLY RDTHAAPVWI RGSLLLFGTF SILLNVFQIG YSVIQINCKS K VEIVFPSI ...String:
GPAGNKASKQ KFCHHCNSRS ASAPPGTSTI HYEKSWLYRH CSLQQRDRQA QKSGQLFSGL LALNVVFLGS AFISSMIFNH VAITLADVW ILLSILKVLC LCWIIYYLLG TSRQPHAVLY RDTHAAPVWI RGSLLLFGTF SILLNVFQIG YSVIQINCKS K VEIVFPSI EILFVATQAF FLWHHSKDCI QVQHNLTRCG LMLTIATNLL LWLLAVTNDS IHMEIESQLR EVEQRLAGNE TD SCACPNT TTCKVFQKGY ILLYPFNTEY CLICCSVLYV MWKNVGRRIS HHHIAHIKPK FKLQGVVFGP LLGAAAVIIG ICV FMMYQI QATGSAPNYQ VFVLYYSYYI VLLPLMCVVA IIGTIIHTLE KRELDTLKNP TRSLDVVLLM GAALGQIAMS YFSI VAIVA TNPRDMLNSL ILSYSVLLIF QYITQNIFII DGLQRQPFAK EEEVSEEHNR EAPDQRRVSV LELGQEFRRV SLSYI HTYS HLGWKRKALK EISFFLVLCN IILWIMPTFG AHPVFENGLQ KSFYGYSTWF AIVNFGLPLS VFYRMHSVGG LLEVYV SA

-
Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: ab initio reconstruction in cryosparc
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 0.6.5)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 43667
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6nf6:
Structure of chicken Otop3 in nanodiscs

+
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