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Yorodumi- PDB-7rro: Structure of the 48-nm repeat doublet microtubule from bovine tra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rro | ||||||
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Title | Structure of the 48-nm repeat doublet microtubule from bovine tracheal cilia | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / cilia / microtubule / dynein / motility | ||||||
Function / homology | Function and homology information mucociliary clearance / outer dynein arm docking complex / regulation of cilium movement / 9+0 motile cilium / outer acrosomal membrane / sperm flagellum assembly / regulation of brood size / establishment of left/right asymmetry / epithelial cilium movement involved in determination of left/right asymmetry / protein localization to motile cilium ...mucociliary clearance / outer dynein arm docking complex / regulation of cilium movement / 9+0 motile cilium / outer acrosomal membrane / sperm flagellum assembly / regulation of brood size / establishment of left/right asymmetry / epithelial cilium movement involved in determination of left/right asymmetry / protein localization to motile cilium / axonemal B tubule inner sheath / manchette assembly / axonemal A tubule inner sheath / regulation of flagellated sperm motility / protein polyglutamylation / 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 / outer dynein arm assembly / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cilium-dependent cell motility / COPI-dependent Golgi-to-ER retrograde traffic / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases activate IQGAPs / regulation of cilium beat frequency involved in ciliary motility / RHO GTPases Activate Formins / cilium movement involved in cell motility / 9+2 motile cilium / Transferases; Transferring phosphorus-containing groups / acrosomal membrane / cilium movement / regulation of cilium assembly / MHC class II antigen presentation / ciliary transition zone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / axoneme assembly / axonemal microtubule / Aggrephagy / flagellated sperm motility / cilium organization / The role of GTSE1 in G2/M progression after G2 checkpoint / ciliary tip / Separation of Sister Chromatids / gamma-tubulin ring complex / 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 / manchette / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / UTP biosynthetic process / CTP biosynthetic process / motile cilium / positive regulation of cell motility / determination of left/right symmetry / GTP biosynthetic process / microtubule organizing center / Neutrophil degranulation / ciliary rootlet / nucleoside diphosphate kinase activity / regulation of neuron projection development / beta-tubulin binding / axoneme / mitotic cytokinesis / spermatid development / centriolar satellite / cilium assembly / cellular response to UV-C / single fertilization / alpha-tubulin binding / sperm flagellum / sperm midpiece / 3'-5' exonuclease activity / Hsp70 protein binding / centriole / acrosomal vesicle / mitotic spindle organization / ciliary basal body / meiotic cell cycle / G protein-coupled receptor binding / lung development / brain development / Hsp90 protein binding / cilium / mitotic spindle / structural constituent of cytoskeleton / SH3 domain binding / spindle / microtubule cytoskeleton organization Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Gui, M. / Anderson, J.R. / Botsch, J.J. / Meleppattu, S. / Singh, S.K. / Zhang, Q. / Brown, A. | ||||||
Funding support | United States, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7rro.cif.gz | 26.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7rro.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7rro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rro_validation.pdf.gz | 21.5 MB | Display | wwPDB validaton report |
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Full document | 7rro_full_validation.pdf.gz | 23.4 MB | Display | |
Data in XML | 7rro_validation.xml.gz | 3.5 MB | Display | |
Data in CIF | 7rro_validation.cif.gz | 5.4 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rr/7rro ftp://data.pdbj.org/pub/pdb/validation_reports/rr/7rro | HTTPS FTP |
-Related structure data
Related structure data | 24664MC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 27 types, 407 molecules 073456ABA0A1A2A3A4AAACAEAGAIAKAMBABCBEBGBIBKBMCACCCE...
-EF-hand domain ... , 2 types, 5 molecules 12TUV
#2: Protein | Mass: 97960.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: F1MMV1 #25: Protein | Mass: 74125.344 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: E1BKH1 |
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-Uncharacterized protein ... , 2 types, 3 molecules 89C
#5: Protein | Mass: 23271.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2TA11 #11: Protein | | Mass: 12361.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32L75 |
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-Cilia and flagella associated protein ... , 3 types, 9 molecules EFabcdefg
#15: Protein | Mass: 36519.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: F6RJC2 #29: Protein | Mass: 65800.328 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32LN4 #30: Protein | Mass: 68719.602 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: E1BKF9 |
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-Coiled-coil domain containing ... , 2 types, 5 molecules H1H2H3op
#19: Protein | Mass: 77675.969 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: F1N2N9 #33: Protein | Mass: 65437.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: E1BJL9 |
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-Non-polymers , 3 types, 451 molecules
#37: Chemical | ChemComp-GTP / #38: Chemical | ChemComp-MG / #39: Chemical | ChemComp-GDP / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Doublet microtubule / Type: COMPLEX / Entity ID: #1-#36 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Bos taurus (cattle) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1267170 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80503 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL |