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- EMDB-20549: Outer Hair Cell, Lateral Wall -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-20549
TitleOuter Hair Cell, Lateral Wall
Map data
Sample
  • Tissue: Cochlea
Biological speciesCavia porcellus (domestic guinea pig)
Methodelectron tomography / cryo EM / negative staining
AuthorsAuer M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders United States
CitationJournal: To Be Published
Title: 3D Ultrastructure of the Cochlear Outer Hair Cell Lateral Wall Revealed By Electron Tomography
Authors: Auer M
History
DepositionAug 1, 2019-
Header (metadata) releaseAug 5, 2020-
Map releaseAug 5, 2020-
UpdateAug 5, 2020-
Current statusAug 5, 2020Processing 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_20549.png

Downloads & links

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Map

FileDownload / File: emd_20549.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Voxel sizeX=Y=Z: 8.1 Å
Density
Minimum - Maximum0 - 5753
Average (Standard dev.)2042.3907 (±202.13263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-290
Dimensions20482048180
Spacing20482048180
CellA: 16588.8 Å / B: 16588.8 Å / C: 1458.0001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z8.10000048828128.10000048828128.1
M x/y/z20482048180
origin x/y/z0.0000.0000.000
length x/y/z16588.80116588.8011458.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS00-290
NC/NR/NS20482048180
D min/max/mean0.0005753.0002042.391

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Supplemental data

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Sample components

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Entire : Cochlea

EntireName: Cochlea
Components
  • Tissue: Cochlea

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Supramolecule #1: Cochlea

SupramoleculeName: Cochlea / type: tissue / ID: 1 / Parent: 0
Source (natural)Organism: Cavia porcellus (domestic guinea pig)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingelectron tomography
Aggregation statetissue

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Sample preparation

BufferpH: 7
StainingType: POSITIVE / Material: Uranyl Acetate
Sugar embeddingMaterial: Epon
GridDetails: unspecified
VitrificationCryogen name: NITROGEN
High pressure freezingInstrument: OTHER
Details: The value given for _emd_high_pressure_freezing.instrument is BALTEC. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', ...Details: The value given for _emd_high_pressure_freezing.instrument is BALTEC. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM HPM100', 'BAL-TEC HPM 010']) so OTHER is written into the XML file.
SectioningUltramicrotomy - Instrument: Leica EM UC6 / Ultramicrotomy - Temperature: 298 K / Ultramicrotomy - Final thickness: 100 nm
Fiducial markerManufacturer: Electron Microscopy Sciences / Diameter: 5 nm

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: TVIPS TEMCAM-F216 (2k x 2k) / Average electron dose: 10.0 e/Å2

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Image processing

Final reconstructionNumber images used: 130

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