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Yorodumi- EMDB-26611: Composite cryo-EM density map of the 8-nm repeat of the human spe... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26611 | |||||||||||||||||||||
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Title | Composite cryo-EM density map of the 8-nm repeat of the human sperm tip singlet microtubule | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information Post-chaperonin tubulin folding pathway / axoneme assembly / axonemal microtubule / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / organelle transport along microtubule / glial cell differentiation / cytoskeleton-dependent intracellular transport / forebrain morphogenesis ...Post-chaperonin tubulin folding pathway / axoneme assembly / axonemal microtubule / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / organelle transport along microtubule / glial cell differentiation / cytoskeleton-dependent intracellular transport / forebrain morphogenesis / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / neuron projection arborization / Gap junction assembly / Formation of tubulin folding intermediates by CCT/TriC / cerebellar cortex morphogenesis / dentate gyrus development / natural killer cell mediated cytotoxicity / COPI-independent Golgi-to-ER retrograde traffic / pyramidal neuron differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / Assembly and cell surface presentation of NMDA receptors / centrosome cycle / COPI-dependent Golgi-to-ER retrograde traffic / motor behavior / response to L-glutamate / ciliary base / smoothened signaling pathway / regulation of synapse organization / locomotory exploration behavior / intercellular bridge / startle response / microtubule polymerization / Recycling pathway of L1 / RHO GTPases activate IQGAPs / sperm flagellum / MHC class I protein binding / Hedgehog 'off' state / response to tumor necrosis factor / cytoplasmic microtubule / microtubule-based process / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / response to mechanical stimulus / Mitotic Prometaphase / homeostasis of number of cells within a tissue / EML4 and NUDC in mitotic spindle formation / condensed chromosome / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / MHC class II antigen presentation / cellular response to calcium ion / adult locomotory behavior / AURKA Activation by TPX2 / acrosomal vesicle / ciliary basal body / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / synapse organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / neuron migration / neuromuscular junction / visual learning / PKR-mediated signaling / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / mitotic spindle / cerebral cortex development / memory / microtubule cytoskeleton organization / recycling endosome / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / calcium-dependent protein binding / extracellular vesicle / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / unfolded protein binding / double-stranded RNA 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 | Homo sapiens (human) / human (human) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.0 Å | |||||||||||||||||||||
Authors | Gui M / Croft JT / Zabeo D / Acharya V / Kollman JM / Burgoyne T / Hoog JL / Brown A | |||||||||||||||||||||
Funding support | United States, Sweden, 6 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26611.map.gz | 373.7 MB | EMDB map data format | |
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Header (meta data) | emd-26611-v30.xml emd-26611.xml | 35.4 KB 35.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26611_fsc.xml | 17.1 KB | Display | FSC data file |
Images | emd_26611.png | 133.6 KB | ||
Masks | emd_26611_msk_1.map | 421.9 MB | Mask map | |
Others | emd_26611_additional_1.map.gz emd_26611_additional_2.map.gz emd_26611_additional_3.map.gz emd_26611_additional_4.map.gz emd_26611_additional_5.map.gz emd_26611_additional_6.map.gz emd_26611_additional_7.map.gz emd_26611_additional_8.map.gz emd_26611_half_map_1.map.gz emd_26611_half_map_2.map.gz | 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 | http://ftp.pdbj.org/pub/emdb/structures/EMD-26611 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26611 | HTTPS FTP |
-Related structure data
Related structure data | 7un1MC 7ungC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26611.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
-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 / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-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: human (human) |
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 |
-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: human (human) |
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 |
-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: human (human) |
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 |
-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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Processing | single particle reconstruction |
Aggregation state | filament |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |