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- EMDB-0444: Cryo-tomogram subregion, Plastin k.o. mouse utricle stereocilia -

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Basic information

Entry
Database: EMDB / ID: EMD-0444
TitleCryo-tomogram subregion, Plastin k.o. mouse utricle stereocilia
Map dataNAD filtered, tomogram subregion, Plastin K.O., primary map
Sample
  • Organelle or cellular component: mouse utricle hair cell stereocilia
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsBarr-Gillespie PG / Auer M
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM051487 United States
National Institutes of Health/National Institute on Deafness and Other Communication DisordersDC005983 United States
National Institutes of Health/National Institute on Deafness and Other Communication DisordersDC011034 United States
National Institutes of Health/National Institute of General Medical SciencesGM121203 United States
National Institutes of Health/National Institute of General Medical SciencesGM115972 United States
National Institutes of Health/Office of the DirectorOD012372 United States
National Institutes of Health/National Institute of General Medical SciencesGM098412-S1 United States
CitationJournal: J Struct Biol / Year: 2020
Title: A cryo-tomography-based volumetric model of the actin core of mouse vestibular hair cell stereocilia lacking plastin 1.
Authors: Junha Song / Roma Patterson / Zoltan Metlagel / Jocelyn F Krey / Samantha Hao / Linshanshan Wang / Brian Ng / Salim Sazzed / Julio Kovacs / Willy Wriggers / Jing He / Peter G Barr-Gillespie / Manfred Auer /
Abstract: Electron cryo-tomography allows for high-resolution imaging of stereocilia in their native state. Because their actin filaments have a higher degree of order, we imaged stereocilia from mice lacking ...Electron cryo-tomography allows for high-resolution imaging of stereocilia in their native state. Because their actin filaments have a higher degree of order, we imaged stereocilia from mice lacking the actin crosslinker plastin 1 (PLS1). We found that while stereocilia actin filaments run 13 nm apart in parallel for long distances, there were gaps of significant size that were stochastically distributed throughout the actin core. Actin crosslinkers were distributed through the stereocilium, but did not occupy all possible binding sites. At stereocilia tips, protein density extended beyond actin filaments, especially on the side of the tip where a tip link is expected to anchor. Along the shaft, repeating density was observed that corresponds to actin-to-membrane connectors. In the taper region, most actin filaments terminated near the plasma membrane. The remaining filaments twisted together to make a tighter bundle than was present in the shaft region; the spacing between them decreased from 13 nm to 9 nm, and the apparent filament diameter decreased from 6.4 to 4.8 nm. Our models illustrate detailed features of distinct structural domains that are present within the stereocilium.
History
DepositionDec 15, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseDec 18, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

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

emd_0444.png

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Map

FileDownload / File: emd_0444.map.gz / Format: CCP4 / Size: 382.8 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationNAD filtered, tomogram subregion, Plastin K.O., primary map
Voxel sizeX=Y=Z: 9.47 Å
Density
Minimum - Maximum1161 - 32767
Average (Standard dev.)19960.232 (±2939.1174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-596-173-241
Dimensions1194348483
Spacing3481194483
CellA: 3295.56 Å / B: 11307.181 Å / C: 4574.0103 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z9.479.47000083752099.47
M x/y/z3481194483
origin x/y/z0.0000.0000.000
length x/y/z3295.56011307.1814574.010
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-173-596-241
NC/NR/NS3481194483
D min/max/mean1161.00032767.00019960.232

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Supplemental data

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Sample components

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Entire : mouse utricle hair cell stereocilia

EntireName: mouse utricle hair cell stereocilia
Components
  • Organelle or cellular component: mouse utricle hair cell stereocilia

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Supramolecule #1: mouse utricle hair cell stereocilia

SupramoleculeName: mouse utricle hair cell stereocilia / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse) / Organ: utricle / Tissue: macula / Organelle: stereocilium / Location in cell: apical surface

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7 / Component - Concentration: 0.154 mol/l / Component - Formula: saline / Component - Name: saline
GridDetails: unspecified
VitrificationCryogen name: ETHANE
Cryo protectantnone
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: SIGMA / Diameter: 10 nm

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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: FEI FALCON II (4k x 4k) / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 80

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