[English] 日本語
Yorodumi
- EMDB-6958: Doublet microtubule of zebrafish sperm axoneme, twister_null mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6958
TitleDoublet microtubule of zebrafish sperm axoneme, twister_null mutant
Map datadoublet microtubule structure from zebrafish sperm flagella, twister_null mutant
Sample
  • Organelle or cellular component: Doublet microtubule from zebrafish sperm flagella, twister_null mutant
Biological speciesDanio rerio (zebrafish)
Methodelectron tomography / cryo EM / Resolution: 43.7 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 2, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseMay 23, 2018-
UpdateDec 12, 2018-
Current statusDec 12, 2018Processing site: PDBj / Status: Released

-
Structure visualization

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

emd_6958.png

Downloads & links

-
Map

FileDownload / File: emd_6958.map.gz / Format: CCP4 / Size: 9.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdoublet microtubule structure from zebrafish sperm flagella, twister_null mutant
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-136.428799999999995 - 270.388849999999991
Average (Standard dev.)10.20443 (±56.14622)
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-136.429270.38910.204

-
Supplemental data

-
Sample components

-
Entire : Doublet microtubule from zebrafish sperm flagella, twister_null mutant

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

-
Supramolecule #1: Doublet microtubule from zebrafish sperm flagella, twister_null mutant

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statefilament

-
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

-
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

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 43.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IMOD / Number images used: 60
CTF correctionSoftware - Name: IMOD
FSC plot (resolution estimation)

+
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