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- EMDB-26611: Composite cryo-EM density map of the 8-nm repeat of the human spe... -
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Basic information
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Title | Composite cryo-EM density map of the 8-nm repeat of the human sperm tip singlet microtubule | |||||||||||||||||||||
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![]() | cilia / microtubule / sperm / cell motility / STRUCTURAL PROTEIN | |||||||||||||||||||||
Function / homology | ![]() Post-chaperonin tubulin folding pathway / axoneme assembly / axonemal microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III ...Post-chaperonin tubulin folding pathway / axoneme assembly / axonemal microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / neuron projection arborization / cytoskeleton-dependent intracellular transport / cerebellar cortex morphogenesis / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / dentate gyrus development / COPI-independent Golgi-to-ER retrograde traffic / pyramidal neuron differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / Assembly and cell surface presentation of NMDA receptors / Kinesins / centrosome cycle / motor behavior / COPI-dependent Golgi-to-ER retrograde traffic / natural killer cell mediated cytotoxicity / response to L-glutamate / ciliary base / smoothened signaling pathway / intercellular bridge / regulation of synapse organization / startle response / cytoplasmic microtubule / locomotory exploration behavior / MHC class I protein binding / Recycling pathway of L1 / microtubule polymerization / microtubule-based process / sperm flagellum / RHO GTPases activate IQGAPs / response to tumor necrosis factor / Hedgehog 'off' state / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / response to mechanical stimulus / Mitotic Prometaphase / condensed chromosome / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / homeostasis of number of cells within a tissue / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to calcium ion / MHC class II antigen presentation / AURKA Activation by TPX2 / adult locomotory behavior / acrosomal vesicle / ciliary basal body / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / synapse organization / neuron migration / visual learning / neuromuscular junction / PKR-mediated signaling / recycling endosome / structural constituent of cytoskeleton / mitotic spindle / memory / cerebral cortex development / microtubule cytoskeleton organization / Aggrephagy / HCMV Early Events / cytoplasmic ribonucleoprotein granule / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / calcium-dependent protein binding / microtubule cytoskeleton / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / double-stranded RNA binding / extracellular vesicle / unfolded protein binding / mitotic cell cycle / gene expression / microtubule binding / neuron apoptotic process / microtubule / cytoskeleton / hydrolase activity / protein heterodimerization activity / cell division / GTPase activity / Neutrophil degranulation Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.0 Å | |||||||||||||||||||||
![]() | Gui M / Croft JT / Zabeo D / Acharya V / Kollman JM / Burgoyne T / Hoog JL / Brown A | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 373.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 35.5 KB 35.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.1 KB | Display | ![]() |
Images | ![]() | 133.6 KB | ||
Masks | ![]() | 421.9 MB | ![]() | |
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 48.6 MB 47.7 MB 337.9 MB 84.2 MB 47.6 MB 47.6 MB 48.3 MB 48.6 MB 340.4 MB 340.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7un1MC ![]() 7ungC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.843 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
+Mask #1
+Additional map: local refined map
+Additional map: local refined map
+Additional map: unsharpened consensus map
+Additional map: unsharpened stitched map
+Additional map: local refined map
+Additional map: local refined map
+Additional map: local refined map
+Additional map: local refined map
+Half map: #2
+Half map: #1
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Sample components
-Entire : Singlet microtubule and associated SPACA9
Entire | Name: Singlet microtubule and associated SPACA9 |
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Components |
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-Supramolecule #1: Singlet microtubule and associated SPACA9
Supramolecule | Name: Singlet microtubule and associated SPACA9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Sperm acrosome-associated protein 9
Macromolecule | Name: Sperm acrosome-associated protein 9 / type: protein_or_peptide / ID: 1 / Number of copies: 33 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.208977 KDa |
Sequence | String: 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 |
-Macromolecule #2: Tubulin beta-4B chain
Macromolecule | Name: Tubulin beta-4B chain / type: protein_or_peptide / ID: 2 / Number of copies: 38 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 49.877824 KDa |
Sequence | String: 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 |
-Macromolecule #3: Tubulin alpha-1A chain
Macromolecule | Name: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 3 / Number of copies: 38 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 50.188441 KDa |
Sequence | String: 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 |
-Macromolecule #4: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 38 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ![]() ChemComp-GDP: |
-Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 38 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ![]() ChemComp-GTP: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 38 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: EMS Lacey Carbon / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
Details | Filaments |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 |