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- EMDB-6954: Doublet microtubule of zebrafish sperm axoneme, WT -

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Basic information

Entry
Database: EMDB / ID: EMD-6954
TitleDoublet microtubule of zebrafish sperm axoneme, WT
Map dataDoublet microtubule structure from zebrafish sperm axoneme, WT
Sample
  • Organelle or cellular component: Doublet microtubule from zebrafish sperm flagella
Biological speciesDanio rerio (zebrafish)
Methodelectron tomography / cryo EM / Resolution: 42.5 Å
AuthorsYamaguchi H / Oda T / Kikkawa M / Takeda H
CitationJournal: Elife / Year: 2018
Title: Systematic studies of all PIH proteins in zebrafish reveal their distinct roles in axonemal dynein assembly.
Authors: Hiroshi Yamaguchi / Toshiyuki Oda / Masahide Kikkawa / Hiroyuki Takeda /
Abstract: Construction of motile cilia/flagella requires cytoplasmic preassembly of axonemal dyneins before transport into cilia. Axonemal dyneins have various subtypes, but the roles of each dynein subtype ...Construction of motile cilia/flagella requires cytoplasmic preassembly of axonemal dyneins before transport into cilia. Axonemal dyneins have various subtypes, but the roles of each dynein subtype and their assembly processes remain elusive in vertebrates. The PIH protein family, consisting of four members, has been implicated in the assembly of different dynein subtypes, although evidence for this idea is sparse. Here, we established zebrafish mutants of all four PIH-protein genes: , , , and , and analyzed the structures of axonemal dyneins in mutant spermatozoa by cryo-electron tomography. Mutations caused the loss of specific dynein subtypes, which was correlated with abnormal sperm motility. We also found organ-specific compositions of dynein subtypes, which could explain the severe motility defects of mutant Kupffer's vesicle cilia. Our data demonstrate that all vertebrate PIH proteins are differently required for cilia/flagella motions and the assembly of axonemal dyneins, assigning specific dynein subtypes to each PIH protein.
History
DepositionMay 1, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseMay 23, 2018-
UpdateDec 12, 2018-
Current statusDec 12, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 50
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 50
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6954.png

Downloads & links

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Map

FileDownload / File: emd_6954.map.gz / Format: CCP4 / Size: 9.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDoublet microtubule structure from zebrafish sperm axoneme, WT
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.2 Å/pix.
x 120 pix.
= 864. Å		7.2 Å/pix.
x 180 pix.
= 1296. Å		7.2 Å/pix.
x 120 pix.
= 864. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 7.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelMovie #1: 50
Minimum - Maximum-125.536330000000007 - 268.715179999999975
Average (Standard dev.)13.900607000000001 (±57.630572999999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180120120
Spacing120180120
CellA: 864.0 Å / B: 1296.0 Å / C: 864.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.27.27.2
M x/y/z120180120
origin x/y/z0.0000.0000.000
length x/y/z864.0001296.000864.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-153-266-98
NX/NY/NZ528514389
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120180120
D min/max/mean-125.536268.71513.901

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Supplemental data

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Sample components

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Entire : Doublet microtubule from zebrafish sperm flagella

EntireName: Doublet microtubule from zebrafish sperm flagella
Components
  • Organelle or cellular component: Doublet microtubule from zebrafish sperm flagella

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Supramolecule #1: Doublet microtubule from zebrafish sperm flagella

SupramoleculeName: Doublet microtubule from zebrafish sperm flagella / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Danio rerio (zebrafish) / Organelle: flagella

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statefilament

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Sample preparation

BufferpH: 7.2
GridModel: Homemade / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP
SectioningOther: NO SECTIONING
Fiducial marker
ManufacturerDiameter
BBInternational15 nm
Aurion15 nm

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Electron microscopy

MicroscopeJEOL 3100FFC
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 30000
Sample stageSpecimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 42.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IMOD / Number images used: 60
CTF correctionSoftware - Name: IMOD
FSC plot (resolution estimation)

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