[English] 日本語
Yorodumi
- EMDB-25051: Tomogram of mouse stereocilia containing PCDH15 molecules labeled... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25051
TitleTomogram of mouse stereocilia containing PCDH15 molecules labeled with 39G7-AuNPs
Map dataTomogram of mouse stereocilia containing PCDH15 molecules labeled with 39G7-AuNPs
Sample
  • Organelle or cellular component: Stereocilia labeled with 39G7-AuNP
    • Organelle or cellular component: Mouse stereocilia
    • Complex: 39G7-AuNP conjugate
Biological speciesMus musculus (house mouse) / Oryctolagus cuniculus (rabbit)
Methodelectron tomography / cryo EM
AuthorsElferich J / Clark S / Ge J / Goehring A / Matsui A / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Citation
Journal: Elife / Year: 2021
Title: Molecular structures and conformations of protocadherin-15 and its complexes on stereocilia elucidated by cryo-electron tomography.
Authors: Johannes Elferich / Sarah Clark / Jingpeng Ge / April Goehring / Aya Matsui / Eric Gouaux /
Abstract: Mechanosensory transduction (MT), the conversion of mechanical stimuli into electrical signals, underpins hearing and balance and is carried out within hair cells in the inner ear. Hair cells harbor ...Mechanosensory transduction (MT), the conversion of mechanical stimuli into electrical signals, underpins hearing and balance and is carried out within hair cells in the inner ear. Hair cells harbor actin-filled stereocilia, arranged in rows of descending heights, where the tips of stereocilia are connected to their taller neighbors by a filament composed of protocadherin 15 (PCDH15) and cadherin 23 (CDH23), deemed the 'tip link.' Tension exerted on the tip link opens an ion channel at the tip of the shorter stereocilia, thus converting mechanical force into an electrical signal. While biochemical and structural studies have provided insights into the molecular composition and structure of isolated portions of the tip link, the architecture, location, and conformational states of intact tip links, on stereocilia, remains unknown. Here, we report in situ cryo-electron microscopy imaging of the tip link in mouse stereocilia. We observe individual PCDH15 molecules at the tip and shaft of stereocilia and determine their stoichiometry, conformational heterogeneity, and their complexes with other filamentous proteins, perhaps including CDH23. The PCDH15 complexes occur in clusters, frequently with more than one copy of PCDH15 at the tip of stereocilia, suggesting that tip links might consist of more than one copy of PCDH15 complexes and, by extension, might include multiple MT complexes.
#1: Journal: Biorxiv / Year: 2021
Title: Molecular structure and conformation of stereocilia tip-links elucidated by cryo-electron tomography
Authors: Elferich J / Clark S / Ge J / Goehring A / Matsui A / Gouaux E
History
DepositionSep 29, 2021-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
UpdateJan 12, 2022-
Current statusJan 12, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Supplemental images

emd_25051.png

Downloads & links

-
Map

FileDownload / File: emd_25051.map.gz / Format: CCP4 / Size: 746.9 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomogram of mouse stereocilia containing PCDH15 molecules labeled with 39G7-AuNPs
Voxel sizeX=Y=Z: 6.611 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)18.38047 (±26.533972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-512
Dimensions14681042512
Spacing10421468512
CellA: 6888.662 Å / B: 9704.948 Å / C: 3384.832 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z6.6116.6116.611
M x/y/z10421468512
origin x/y/z0.0000.0000.000
length x/y/z6888.6629704.9483384.832
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS00-512
NC/NR/NS10421468512
D min/max/mean-128.000127.00018.380

-
Supplemental data

-
Sample components

-
Entire : Stereocilia labeled with 39G7-AuNP

EntireName: Stereocilia labeled with 39G7-AuNP
Components
  • Organelle or cellular component: Stereocilia labeled with 39G7-AuNP
    • Organelle or cellular component: Mouse stereocilia
    • Complex: 39G7-AuNP conjugate

-
Supramolecule #1: Stereocilia labeled with 39G7-AuNP

SupramoleculeName: Stereocilia labeled with 39G7-AuNP / type: organelle_or_cellular_component / ID: 1 / Parent: 0

-
Supramolecule #2: Mouse stereocilia

SupramoleculeName: Mouse stereocilia / type: organelle_or_cellular_component / ID: 2 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

-
Supramolecule #3: 39G7-AuNP conjugate

SupramoleculeName: 39G7-AuNP conjugate / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statetissue

-
Sample preparation

BufferpH: 7.4 / Details: DMEM/F12
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: PELCO / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 41 / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionSoftware - Name: TomoAlign (ver. Jan2019) / Number images used: 41
CTF correctionSoftware - Name: IMOD

+
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