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Open data
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Basic information
Entry | Database: PDB / ID: 9ntm | |||||||||
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Title | SPEF1 bound to 14-pf microtubule | |||||||||
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![]() | PROTEIN BINDING / microtubules / spef1 / seam | |||||||||
Function / homology | ![]() axonemal central apparatus / axonemal central apparatus assembly / regulation of Wnt signaling pathway, planar cell polarity pathway / 9+2 motile cilium / cilium movement / ciliary tip / negative regulation of microtubule depolymerization / filopodium assembly / microtubule bundle formation / lamellipodium assembly ...axonemal central apparatus / axonemal central apparatus assembly / regulation of Wnt signaling pathway, planar cell polarity pathway / 9+2 motile cilium / cilium movement / ciliary tip / negative regulation of microtubule depolymerization / filopodium assembly / microtubule bundle formation / lamellipodium assembly / regulation of cytoskeleton organization / microvillus / axoneme / host cell membrane / microtubule-based process / cytoplasmic microtubule / stress fiber / cellular response to interleukin-4 / bioluminescence / generation of precursor metabolites and energy / filopodium / structural constituent of cytoskeleton / microtubule cytoskeleton organization / cell migration / mitotic cell cycle / lamellipodium / double-stranded RNA binding / actin binding / microtubule cytoskeleton / basolateral plasma membrane / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cilium / apical plasma membrane / symbiont entry into host cell / GTPase activity / viral envelope / ubiquitin protein ligase binding / GTP binding / virion attachment to host cell / virion membrane / metal ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7.1 Å | |||||||||
![]() | Legal, T. / Bui, K.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the ciliary tip central pair reveals the unique role of the microtubule-seam binding protein SPEF1. Authors: Thibault Legal / Ewa Joachimiak / Mireya Parra / Wang Peng / Amanda Tam / Corbin Black / Mayukh Guha / Chau Anh Nguyen / Avrin Ghanaeian / Melissa Valente-Paterno / Gary Brouhard / Jacek ...Authors: Thibault Legal / Ewa Joachimiak / Mireya Parra / Wang Peng / Amanda Tam / Corbin Black / Mayukh Guha / Chau Anh Nguyen / Avrin Ghanaeian / Melissa Valente-Paterno / Gary Brouhard / Jacek Gaertig / Dorota Wloga / Khanh Huy Bui / ![]() ![]() ![]() Abstract: Motile cilia are unique organelles with the ability to move autonomously. The force generated by beating cilia propels cells and moves fluids. The ciliary skeleton is made of peripheral doublet ...Motile cilia are unique organelles with the ability to move autonomously. The force generated by beating cilia propels cells and moves fluids. The ciliary skeleton is made of peripheral doublet microtubules and a central pair (CP) with a distinct structure at the tip. In this study, we present a high-resolution structure of the CP in the ciliary tip of the ciliate Tetrahymena thermophila and identify several tip proteins that bind and form unique patterns on both microtubules of the tip CP. Two of those proteins that contain tubulin polymerization-promoting protein (TPPP)-like domains, TLP1 and TLP2, bind to high curvature regions of the microtubule. TLP2, which contains two TPPP-like domains, is an unusually long protein that wraps laterally around half a microtubule and forms the bridge between the two microtubules. Moreover, we found that the conserved protein SPEF1 binds to both microtubule seams and crosslinked the two microtubules. In vitro, human SPEF1 binds to the microtubule seam as visualized by cryoelectron tomography and subtomogram averaging. Single-molecule microtubule dynamics assays indicate that SPEF1 stabilizes microtubules in vitro. Together, these data show that the proteins in the tip CP maintain stable microtubule structures and play important roles in maintaining the integrity of the axoneme. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 6.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 9.7 MB | Display | ![]() |
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Full document | ![]() | 10.7 MB | Display | |
Data in XML | ![]() | 1 MB | Display | |
Data in CIF | ![]() | 1.5 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 49760MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 3 types, 89 molecules 1A1B1C1D1EAAACAEBABCBECACCCEDADCDEEAECEEFAFCFEGAGCGEHAHCHEIA...
#1: Protein | Mass: 44324.262 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SPEF1, C20orf28, G, GFP / Production host: ![]() ![]() #2: Protein | Mass: 50204.445 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 49983.824 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 4 types, 168 molecules 






#4: Chemical | ChemComp-GTP / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-GDP / #7: Chemical | ChemComp-TA1 / |
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-Details
Has ligand of interest | N |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: subtomogram averaging |
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Sample preparation
Component | Name: 14-protofilament microtubule bound by SPEF1 CH-domain / Type: COMPLEX / Entity ID: #2-#3, #1 / Source: MULTIPLE SOURCES | ||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() ![]() | ||||||||||||
Buffer solution | pH: 6.8 | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm |
Image recording | Electron dose: 4 e/Å2 / Avg electron dose per subtomogram: 164 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.21_5207 / Category: model refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9625 / Symmetry type: POINT |
EM volume selection | Num. of tomograms: 58 / Num. of volumes extracted: 20342 |