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Yorodumi- EMDB-24664: Composite cryo-EM density map of the 48-nm repeat doublet microtu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24664 | |||||||||
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Title | Composite cryo-EM density map of the 48-nm repeat doublet microtubule from bovine tracheal cilia | |||||||||
Map data | ||||||||||
Sample |
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Keywords | cilia / microtubule / dynein / motility / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information regulation of cilium beat frequency / mucociliary clearance / outer dynein arm docking complex / sperm flagellum assembly / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / protein localization to motile cilium / manchette assembly / axonemal B tubule inner sheath ...regulation of cilium beat frequency / mucociliary clearance / outer dynein arm docking complex / sperm flagellum assembly / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / protein localization to motile cilium / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / epithelial cilium movement involved in determination of left/right asymmetry / protein polyglutamylation / sperm axoneme assembly / positive regulation of feeding behavior / 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 / cerebrospinal fluid circulation / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / outer dynein arm assembly / cilium-dependent cell motility / 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 / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / 9+2 motile cilium / Transferases; Transferring phosphorus-containing groups / acrosomal membrane / MHC class II antigen presentation / ciliary transition zone / regulation of cilium assembly / cilium movement / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / axoneme assembly / Aggrephagy / axonemal microtubule / left/right axis specification / cilium organization / gamma-tubulin ring complex / The role of GTSE1 in G2/M progression after G2 checkpoint / flagellated sperm motility / 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 / ventricular system development / manchette / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / positive regulation of cilium assembly / UTP biosynthetic process / CTP biosynthetic process / motile cilium / positive regulation of cell motility / determination of left/right symmetry / microtubule organizing center / Neutrophil degranulation / intermediate filament / GTP biosynthetic process / nucleoside diphosphate kinase activity / ciliary base / regulation of neuron projection development / beta-tubulin binding / axoneme / mitotic cytokinesis / centriolar satellite / spermatid development / cilium assembly / alpha-tubulin binding / cellular response to UV-C / sperm flagellum / single fertilization / sperm midpiece / Hsp70 protein binding / 3'-5' exonuclease activity / centriole / mitotic spindle organization / acrosomal vesicle / lung development / ciliary basal body / G protein-coupled receptor binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / brain development / cilium / structural constituent of cytoskeleton / mitotic spindle / spindle pole Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Gui M / Anderson JR / Botsch JJ / Meleppattu S / Singh SK / Zhang Q / Brown A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell / Year: 2021 Title: De novo identification of mammalian ciliary motility proteins using cryo-EM. Authors: Miao Gui / Hannah Farley / Priyanka Anujan / Jacob R Anderson / Dale W Maxwell / Jonathan B Whitchurch / J Josephine Botsch / Tao Qiu / Shimi Meleppattu / Sandeep K Singh / Qi Zhang / James ...Authors: Miao Gui / Hannah Farley / Priyanka Anujan / Jacob R Anderson / Dale W Maxwell / Jonathan B Whitchurch / J Josephine Botsch / Tao Qiu / Shimi Meleppattu / Sandeep K Singh / Qi Zhang / James Thompson / Jane S Lucas / Colin D Bingle / Dominic P Norris / Sudipto Roy / Alan Brown / Abstract: Dynein-decorated doublet microtubules (DMTs) are critical components of the oscillatory molecular machine of cilia, the axoneme, and have luminal surfaces patterned periodically by microtubule inner ...Dynein-decorated doublet microtubules (DMTs) are critical components of the oscillatory molecular machine of cilia, the axoneme, and have luminal surfaces patterned periodically by microtubule inner proteins (MIPs). Here we present an atomic model of the 48-nm repeat of a mammalian DMT, derived from a cryoelectron microscopy (cryo-EM) map of the complex isolated from bovine respiratory cilia. The structure uncovers principles of doublet microtubule organization and features specific to vertebrate cilia, including previously unknown MIPs, a luminal bundle of tektin filaments, and a pentameric dynein-docking complex. We identify a mechanism for bridging 48- to 24-nm periodicity across the microtubule wall and show that loss of the proteins involved causes defective ciliary motility and laterality abnormalities in zebrafish and mice. Our structure identifies candidate genes for diagnosis of ciliopathies and provides a framework to understand their functions in driving ciliary motility. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
-Validation report
Summary document | emd_24664_validation.pdf.gz | 613.6 KB | Display | EMDB validaton report |
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Full document | emd_24664_full_validation.pdf.gz | 613.2 KB | Display | |
Data in XML | emd_24664_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | emd_24664_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24664 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24664 | HTTPS FTP |
-Related structure data
Related structure data | 7rroMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24664.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Additional map: consensus map
+Additional map: local refined fragment 6-1
+Additional map: local refined fragment 6-3
+Additional map: local refined fragment 8-1
+Additional map: local refined fragment 4-3
+Additional map: local refined fragment 2-2
+Additional map: local refined fragment 2-3
+Additional map: local refined fragment 3-3
+Additional map: local refined fragment 10-3
+Additional map: local refined fragment 4-1
+Additional map: deepemhancer postprocessing map
+Additional map: local refined fragment of 8 tektin filaments 1
+Additional map: local refined fragment 10-1
+Additional map: local refined fragment 4-2
+Additional map: local refined fragment 1-2
+Additional map: local refined fragment of 8 tektin filaments 3
+Additional map: local refined fragment 7-3
+Additional map: local refined fragment 2-1
+Additional map: local refined fragment 3-2
+Additional map: local refined fragment 8-2
+Additional map: local refined fragment 7-1
+Additional map: local refined fragment 10-2
+Additional map: local refined fragment 8-3
+Additional map: local refined fragment 5-2
+Additional map: local refined fragment 3-1
+Additional map: local refined fragment 9-2
+Additional map: local refined fragment 9-1
+Additional map: local refined fragment of Pierce1/2 region 2
+Additional map: multi-body local refined fragment of ODA-DC
+Additional map: local refined fragment 1-3
+Additional map: local refined fragment of Pierce1/2 region 1
+Additional map: local refined fragment 9-3
+Additional map: Overall cylinder mask
+Additional map: local refined fragment of 8 tektin filaments 2
+Additional map: local refined fragment 6-2
+Additional map: local refined fragment 5-3
+Additional map: local refined fragment 7-2
+Additional map: local refined fragment 5-1
+Additional map: local refined fragment 1-1
-Sample components
+Entire : Doublet microtubule
+Supramolecule #1: Doublet microtubule
+Macromolecule #1: Protein C9orf135 homolog
+Macromolecule #2: EF-hand domain family member B
+Macromolecule #3: Methyl-CpG binding domain protein 1
+Macromolecule #4: Nucleoside diphosphate kinase 7
+Macromolecule #5: Uncharacterized protein C1orf158 homolog
+Macromolecule #6: Meiosis-specific nuclear structural protein 1
+Macromolecule #7: Tektin-1
+Macromolecule #8: Tubulin alpha-1D chain
+Macromolecule #9: Tubulin beta-4B chain
+Macromolecule #10: Tektin-2
+Macromolecule #11: Uncharacterized protein C1orf189 homolog
+Macromolecule #12: Tektin-3
+Macromolecule #13: Sperm associated antigen 8
+Macromolecule #14: Tektin-4
+Macromolecule #15: Cilia and flagella associated protein 161
+Macromolecule #16: TEKTIP1
+Macromolecule #17: Pierce2
+Macromolecule #18: Protein FAM166B
+Macromolecule #19: Coiled-coil domain containing 114
+Macromolecule #20: Outer dynein arm-docking complex subunit 3
+Macromolecule #21: Armadillo repeat containing 4
+Macromolecule #22: TTC25 protein
+Macromolecule #23: EF-hand calcium-binding domain-containing protein 1
+Macromolecule #24: RIB43A-like with coiled-coils protein 2
+Macromolecule #25: EF-hand domain containing 1
+Macromolecule #26: EFHC2
+Macromolecule #27: Cilia- and flagella-associated protein 20
+Macromolecule #28: PACRG protein
+Macromolecule #29: Cilia and flagella associated protein 45
+Macromolecule #30: Cilia and flagella associated protein 52
+Macromolecule #31: Enkurin, TRPC channel interacting protein
+Macromolecule #32: Protein Flattop
+Macromolecule #33: Coiled-coil domain containing 173
+Macromolecule #34: Chromosome 3 C1orf194 homolog
+Macromolecule #35: EFCAB6
+Macromolecule #36: Pierce1
+Macromolecule #37: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #38: MAGNESIUM ION
+Macromolecule #39: GUANOSINE-5'-DIPHOSPHATE
-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 | Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-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: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7rro: |