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- EMDB-6958: Doublet microtubule of zebrafish sperm axoneme, twister_null mutant -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6958 | |||||||||
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Title | Doublet microtubule of zebrafish sperm axoneme, twister_null mutant | |||||||||
![]() | doublet microtubule structure from zebrafish sperm flagella, twister_null mutant | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | electron tomography / cryo EM / Resolution: 43.7 Å | |||||||||
![]() | Yamaguchi H / Oda T / Kikkawa M / Takeda H | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 9.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.6 KB 10.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.4 KB | Display | ![]() |
Images | ![]() | 70.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6954C ![]() 6955C ![]() 6956C ![]() 6957C ![]() 6959C ![]() 6960C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | doublet microtubule structure from zebrafish sperm flagella, twister_null mutant | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Doublet microtubule from zebrafish sperm flagella, twister_null mutant
Entire | Name: Doublet microtubule from zebrafish sperm flagella, twister_null mutant |
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Components |
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-Supramolecule #1: Doublet microtubule from zebrafish sperm flagella, twister_null mutant
Supramolecule | Name: Doublet microtubule from zebrafish sperm flagella, twister_null mutant type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | electron tomography |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.2 | ||||||
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Grid | Model: Homemade / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP | ||||||
Sectioning | Other: NO SECTIONING | ||||||
Fiducial marker |
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Electron microscopy
Microscope | JEOL 3100FFC |
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Specialist optics | Energy filter - Name: In-column Omega Filter |
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 30000 |
Sample stage | Specimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER Cooling holder cryogen: NITROGEN |