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- EMDB-17188: bovine sperm endpiece singlet microtubules (one tubulin dimer and... -

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Entry
Database: EMDB / ID: EMD-17188
Titlebovine sperm endpiece singlet microtubules (one tubulin dimer and associated microtubule inner proteins)
Map datacryo-EM map obtained after symmetry expansion showing two tubulin dimers along a protofilament from bovine sperm endpiece microtubules
Sample
  • Complex: tubulin heterodimer with associated microtubule inner proteins SPACA9 and SAXO1
    • Protein or peptide: Tubulin beta-4B chain
    • Protein or peptide: Stabilizer of axonemal microtubules 1
    • Protein or peptide: Sperm acrosome associated 9
    • Protein or peptide: Tubulin alpha-3 chain
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
Keywordsmicrotubule / microtubule inner protein / sperm / cilia / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / COPI-dependent Golgi-to-ER retrograde traffic ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases activate IQGAPs / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases Activate Formins / cold acclimation / MHC class II antigen presentation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / axoneme assembly / axonemal microtubule / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of NuMA to mitotic centrosomes / Regulation of PLK1 Activity at G2/M Transition / positive regulation of cilium assembly / Hedgehog 'off' state / Neutrophil degranulation / cellular response to cold / ciliary base / intercellular bridge / sperm flagellum / centriole / acrosomal vesicle / ciliary basal body / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / mitotic spindle / microtubule cytoskeleton organization / calcium-dependent protein binding / double-stranded RNA binding / mitotic cell cycle / microtubule binding / microtubule / protein stabilization / cytoskeleton / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Stabilizer of axonemal microtubules 1/2 / Sperm acrosome-associated protein 9 / Sperm acrosome-associated protein 9 / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain ...Stabilizer of axonemal microtubules 1/2 / Sperm acrosome-associated protein 9 / Sperm acrosome-associated protein 9 / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Sperm acrosome associated 9 / Stabilizer of axonemal microtubules 1 / Tubulin alpha-3 chain / Tubulin beta-4B chain
Similarity search - Component
Biological speciesBos taurus (cattle) / cattle (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLeung MR / Zeev-Ben-Mordehai T
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)740.018.007 Netherlands
CitationJournal: Cell / Year: 2023
Title: Structural specializations of the sperm tail.
Authors: Miguel Ricardo Leung / Jianwei Zeng / Xiangli Wang / Marc C Roelofs / Wei Huang / Riccardo Zenezini Chiozzi / Johannes F Hevler / Albert J R Heck / Susan K Dutcher / Alan Brown / Rui Zhang / ...Authors: Miguel Ricardo Leung / Jianwei Zeng / Xiangli Wang / Marc C Roelofs / Wei Huang / Riccardo Zenezini Chiozzi / Johannes F Hevler / Albert J R Heck / Susan K Dutcher / Alan Brown / Rui Zhang / Tzviya Zeev-Ben-Mordehai /
Abstract: Sperm motility is crucial to reproductive success in sexually reproducing organisms. Impaired sperm movement causes male infertility, which is increasing globally. Sperm are powered by a microtubule- ...Sperm motility is crucial to reproductive success in sexually reproducing organisms. Impaired sperm movement causes male infertility, which is increasing globally. Sperm are powered by a microtubule-based molecular machine-the axoneme-but it is unclear how axonemal microtubules are ornamented to support motility in diverse fertilization environments. Here, we present high-resolution structures of native axonemal doublet microtubules (DMTs) from sea urchin and bovine sperm, representing external and internal fertilizers. We identify >60 proteins decorating sperm DMTs; at least 15 are sperm associated and 16 are linked to infertility. By comparing DMTs across species and cell types, we define core microtubule inner proteins (MIPs) and analyze evolution of the tektin bundle. We identify conserved axonemal microtubule-associated proteins (MAPs) with unique tubulin-binding modes. Additionally, we identify a testis-specific serine/threonine kinase that links DMTs to outer dense fibers in mammalian sperm. Our study provides structural foundations for understanding sperm evolution, motility, and dysfunction at a molecular level.
History
DepositionApr 21, 2023-
Header (metadata) releaseJul 5, 2023-
Map releaseJul 5, 2023-
UpdateJul 5, 2023-
Current statusJul 5, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17188.png

Downloads & links

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Map

FileDownload / File: emd_17188.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map obtained after symmetry expansion showing two tubulin dimers along a protofilament from bovine sperm endpiece microtubules
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 320 pix.
= 434.88 Å		1.36 Å/pix.
x 320 pix.
= 434.88 Å		1.36 Å/pix.
x 320 pix.
= 434.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.359 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.101278245 - 0.16951378
Average (Standard dev.)0.00007009133 (±0.0021591117)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 434.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half-map1

Fileemd_17188_half_map_1.map
Annotationhalf-map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map2

Fileemd_17188_half_map_2.map
Annotationhalf-map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : tubulin heterodimer with associated microtubule inner proteins SP...

EntireName: tubulin heterodimer with associated microtubule inner proteins SPACA9 and SAXO1
Components
  • Complex: tubulin heterodimer with associated microtubule inner proteins SPACA9 and SAXO1
    • Protein or peptide: Tubulin beta-4B chain
    • Protein or peptide: Stabilizer of axonemal microtubules 1
    • Protein or peptide: Sperm acrosome associated 9
    • Protein or peptide: Tubulin alpha-3 chain
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION

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Supramolecule #1: tubulin heterodimer with associated microtubule inner proteins SP...

SupramoleculeName: tubulin heterodimer with associated microtubule inner proteins SPACA9 and SAXO1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Bos taurus (cattle)

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Macromolecule #1: Tubulin beta-4B chain

MacromoleculeName: Tubulin beta-4B chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 49.877824 KDa
SequenceString: MREIVHLQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLERINVY YNEATGGKYV PRAVLVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHLQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLERINVY YNEATGGKYV PRAVLVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEGE FEEEAEEEVA

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Macromolecule #2: Stabilizer of axonemal microtubules 1

MacromoleculeName: Stabilizer of axonemal microtubules 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 54.67207 KDa
SequenceString: MAPTKGKCVC ELCSCGRHHC PHLPTKIYDK TEKPCLLSEY TENYPVYHSY LPRESFKPKM DYQRACTPME GLTTSRRDFG PHKVLPVKI HQPNPFVPSE ENMDLQTTYK QDYNPYPLCR VDPFKPRDSK YPCGDKMESL PTYKADYLPW NQPRRELLRP P HHYRPAST ...String:
MAPTKGKCVC ELCSCGRHHC PHLPTKIYDK TEKPCLLSEY TENYPVYHSY LPRESFKPKM DYQRACTPME GLTTSRRDFG PHKVLPVKI HQPNPFVPSE ENMDLQTTYK QDYNPYPLCR VDPFKPRDSK YPCGDKMESL PTYKADYLPW NQPRRELLRP P HHYRPAST KFDSRTTQQD DYSMKGLVNT RSCKPPAVPK LCNVPLEDLT NYKMSYVAHP LEKRFVHESE KFRPCEIPFE SL TTHKESY RGLMGEPAKS LKPPARPYGL DTPFSNTTEF RDKYQAWPTP QVFSKPPSMY VPPEEKMDLL TTVQTHYTYP KGA PAESCR PALSVKKGGR FEGSTTTKED YKQWASTRTE PAKPIPQLNL PTEPLDCLTT ARAHYVPHLP MMTKSCKPVW SGPQ GNIPV EGQTTYTISF TPKEMSRCLA SYPEPPGYIF EEIDALGHRI YRPVSQTGSR RSSRFSVGDS ENPNQQELTV SA

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Macromolecule #3: Sperm acrosome associated 9

MacromoleculeName: Sperm acrosome associated 9 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 25.174801 KDa
SequenceString: MMNEVKESLR SVEQKYKIFQ QQQFTFIGAL EHCRENAHDK IRPISSIGQV QSYMEHHCSN STDRRILLMF LDICSELSKL CQHFEALHA GTPVTNNLLE KCKTLVSQSN DLSSLRAKYP HDVVNHLSCD EARNHYGGVV SLIPIILDLM KEWVAHSEKL P RKALQQVS ...String:
MMNEVKESLR SVEQKYKIFQ QQQFTFIGAL EHCRENAHDK IRPISSIGQV QSYMEHHCSN STDRRILLMF LDICSELSKL CQHFEALHA GTPVTNNLLE KCKTLVSQSN DLSSLRAKYP HDVVNHLSCD EARNHYGGVV SLIPIILDLM KEWVAHSEKL P RKALQQVS EPQAATRATA HAPQASGTQP QLRKQNCGQL IQNIPKPGGK DQGSSKPPWR PPGGKL

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Macromolecule #4: Tubulin alpha-3 chain

MacromoleculeName: Tubulin alpha-3 chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 49.978344 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVVDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIVDLVL DRIRKLADLC TGLQGFLIFH SFGGGTGSGF ASLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVVDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIVDLVL DRIRKLADLC TGLQGFLIFH SFGGGTGSGF ASLLMERLSV D YGKKSKLE FAIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCM LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKLD LMYA KRAFV HWYVGEGMEE GEFSEAREDL AALEKDYEEV GVDSVEAEAE EGEEY

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Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

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Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.3
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

12068

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 240292

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