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- EMDB-26611: Composite cryo-EM density map of the 8-nm repeat of the human spe... -

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Entry
Database: EMDB / ID: EMD-26611
TitleComposite cryo-EM density map of the 8-nm repeat of the human sperm tip singlet microtubule
Map data
Sample
  • Complex: Singlet microtubule and associated SPACA9
    • Protein or peptide: Sperm acrosome-associated protein 9
    • Protein or peptide: Tubulin beta-4B chain
    • Protein or peptide: Tubulin alpha-1A chain
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordscilia / microtubule / sperm / cell motility / STRUCTURAL PROTEIN
Function / homology
Function and homology information


axonemal microtubule doublet inner sheath / axoneme assembly / Post-chaperonin tubulin folding pathway / organelle transport along microtubule / axonemal microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / forebrain morphogenesis ...axonemal microtubule doublet inner sheath / axoneme assembly / Post-chaperonin tubulin folding pathway / organelle transport along microtubule / axonemal microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / forebrain morphogenesis / glial cell differentiation / neuron projection arborization / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / flagellated sperm motility / cerebellar cortex morphogenesis / Formation of tubulin folding intermediates by CCT/TriC / dentate gyrus development / COPI-independent Golgi-to-ER retrograde traffic / Gap junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / centrosome cycle / Assembly and cell surface presentation of NMDA receptors / pyramidal neuron differentiation / motor behavior / COPI-dependent Golgi-to-ER retrograde traffic / response to L-glutamate / natural killer cell mediated cytotoxicity / smoothened signaling pathway / regulation of synapse organization / ciliary base / intercellular bridge / startle response / locomotory exploration behavior / MHC class I protein binding / Recycling pathway of L1 / microtubule polymerization / sperm flagellum / response to tumor necrosis factor / RHO GTPases activate IQGAPs / cytoplasmic microtubule / Hedgehog 'off' state / COPI-mediated anterograde transport / microtubule-based process / response to mechanical stimulus / Activation of AMPK downstream of NMDARs / Mitotic Prometaphase / condensed chromosome / EML4 and NUDC in mitotic spindle formation / homeostasis of number of cells within a tissue / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / cellular response to calcium ion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / acrosomal vesicle / ciliary basal body / adult locomotory behavior / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / intracellular protein transport / synapse organization / neuron migration / visual learning / neuromuscular junction / PKR-mediated signaling / recycling endosome / cerebral cortex development / structural constituent of cytoskeleton / memory / mitotic spindle / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / HCMV Early Events / Aggrephagy / calcium-dependent protein binding / Separation of Sister Chromatids / azurophil granule lumen / microtubule cytoskeleton / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / unfolded protein binding / extracellular vesicle / mitotic cell cycle / double-stranded RNA binding / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / gene expression / neuron apoptotic process / microtubule / cytoskeleton / hydrolase activity / protein heterodimerization activity / cell division
Similarity search - Function
Sperm acrosome-associated protein 9 / Sperm acrosome-associated protein 9 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site ...Sperm acrosome-associated protein 9 / Sperm acrosome-associated protein 9 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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
Tubulin beta-4B chain / Tubulin alpha-1A chain / Sperm acrosome-associated protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsGui M / Croft JT / Zabeo D / Acharya V / Kollman JM / Burgoyne T / Hoog JL / Brown A
Funding support United States, Sweden, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141109 United States
Swedish Research Council2015-05427 Sweden
Swedish Research Council2019-04004 Sweden
Smith Family Foundation United States
Pew Charitable Trusts United States
Charles A. King Trust Postdoctoral Research Fellowship United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: SPACA9 is a lumenal protein of human ciliary singlet and doublet microtubules.
Authors: Miao Gui / Jacob T Croft / Davide Zabeo / Vajradhar Acharya / Justin M Kollman / Thomas Burgoyne / Johanna L Höög / Alan Brown /
Abstract: The cilium-centrosome complex contains triplet, doublet, and singlet microtubules. The lumenal surfaces of each microtubule within this diverse array are decorated by microtubule inner proteins ...The cilium-centrosome complex contains triplet, doublet, and singlet microtubules. The lumenal surfaces of each microtubule within this diverse array are decorated by microtubule inner proteins (MIPs). Here, we used single-particle cryo-electron microscopy methods to build atomic models of two types of human ciliary microtubule: the doublet microtubules of multiciliated respiratory cells and the distal singlet microtubules of monoflagellated human spermatozoa. We discover that SPACA9 is a polyspecific MIP capable of binding both microtubule types. SPACA9 forms intralumenal striations in the B tubule of respiratory doublet microtubules and noncontinuous spirals in sperm singlet microtubules. By acquiring new and reanalyzing previous cryo-electron tomography data, we show that SPACA9-like intralumenal striations are common features of different microtubule types in animal cilia. Our structures provide detailed references to help rationalize ciliopathy-causing mutations and position cryo-EM as a tool for the analysis of samples obtained directly from ciliopathy patients.
History
DepositionApr 8, 2022-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26611.png

Downloads & links

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Map

FileDownload / File: emd_26611.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 480 pix.
= 404.64 Å		0.84 Å/pix.
x 480 pix.
= 404.64 Å		0.84 Å/pix.
x 480 pix.
= 404.64 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.843 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0017753531 - 2.386037
Average (Standard dev.)0.015121182 (±0.09040541)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 404.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26611_msk_1.map
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Additional map: local refined map

Fileemd_26611_additional_1.map
Annotationlocal refined map
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Additional map: local refined map

Fileemd_26611_additional_2.map
Annotationlocal refined map
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Additional map: unsharpened consensus map

Fileemd_26611_additional_3.map
Annotationunsharpened consensus map
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Additional map: unsharpened stitched map

Fileemd_26611_additional_4.map
Annotationunsharpened stitched map
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Additional map: local refined map

Fileemd_26611_additional_5.map
Annotationlocal refined map
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Additional map: local refined map

Fileemd_26611_additional_6.map
Annotationlocal refined map
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Additional map: local refined map

Fileemd_26611_additional_7.map
Annotationlocal refined map
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Additional map: local refined map

Fileemd_26611_additional_8.map
Annotationlocal refined map
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Half map: #2

Fileemd_26611_half_map_1.map
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Half map: #1

Fileemd_26611_half_map_2.map
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Sample components

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Entire : Singlet microtubule and associated SPACA9

EntireName: Singlet microtubule and associated SPACA9
Components
  • Complex: Singlet microtubule and associated SPACA9
    • Protein or peptide: Sperm acrosome-associated protein 9
    • Protein or peptide: Tubulin beta-4B chain
    • Protein or peptide: Tubulin alpha-1A chain
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Singlet microtubule and associated SPACA9

SupramoleculeName: Singlet microtubule and associated SPACA9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sperm acrosome-associated protein 9

MacromoleculeName: Sperm acrosome-associated protein 9 / type: protein_or_peptide / ID: 1 / Number of copies: 33 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.208977 KDa
SequenceString: MNEVKESLRS IEQKYKLFQQ QQLTFTAALE HCRENAHDKI RPISSIGQVQ SYMEHYCNSS TDRRVLLMFL DICSELNKLC QHFEAVHSG TPVTNNLLEK CKTLVSQSND LSSLRAKYPH DVVNHLSCDE ARNHYGGVVS LIPLILDLMK EWIAHSEKLP R KVLQHVSE ...String:
MNEVKESLRS IEQKYKLFQQ QQLTFTAALE HCRENAHDKI RPISSIGQVQ SYMEHYCNSS TDRRVLLMFL DICSELNKLC QHFEAVHSG TPVTNNLLEK CKTLVSQSND LSSLRAKYPH DVVNHLSCDE ARNHYGGVVS LIPLILDLMK EWIAHSEKLP R KVLQHVSE PQAHQESTRG AARPAQAIGT QPRATKHKCR QLTKASLKPR GCSKPPWRPP GGKL

UniProtKB: Sperm acrosome-associated protein 9

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Macromolecule #2: Tubulin beta-4B chain

MacromoleculeName: Tubulin beta-4B chain / type: protein_or_peptide / ID: 2 / Number of copies: 38 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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

UniProtKB: Tubulin beta-4B chain

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Macromolecule #3: Tubulin alpha-1A chain

MacromoleculeName: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 3 / Number of copies: 38 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.188441 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1A chain

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Macromolecule #4: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 38 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

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

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Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 38 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

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

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 38 / 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: 7.4
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE
DetailsFilaments

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: Modified map of human respiratory doublet microtubule in the same study
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 21990
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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