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Yorodumi- PDB-8c5c: microtubule decorated with tubulin oligomers in presence of APC C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c5c | ||||||
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Title | microtubule decorated with tubulin oligomers in presence of APC C-terminal domain. (here only map corresponding to the 13-pf microtubule is represented) | ||||||
Components |
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Keywords | CELL CYCLE / cytoskeleton / microtubule | ||||||
Function / homology | Function and homology information 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 / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / COPI-dependent Golgi-to-ER retrograde traffic ...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 / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / 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 / MHC class II antigen presentation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Recruitment of NuMA to mitotic centrosomes / Hedgehog 'off' state / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / neuron migration / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / microtubule / GTPase activity / GTP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5.3 Å | ||||||
Authors | Serre, L. / Arnal, I. | ||||||
Funding support | France, 1items
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Citation | Journal: J Cell Sci / Year: 2023 Title: The mitotic role of adenomatous polyposis coli requires its bilateral interaction with tubulin and microtubules. Authors: Laurence Serre / Julie Delaroche / Angélique Vinit / Guy Schoehn / Eric Denarier / Anne Fourest-Lieuvin / Isabelle Arnal / Abstract: Adenomatous polyposis coli (APC) is a scaffold protein with tumour suppressor properties. Mutations causing the loss of its C-terminal domain (APC-C), which bears cytoskeleton-regulating sequences, ...Adenomatous polyposis coli (APC) is a scaffold protein with tumour suppressor properties. Mutations causing the loss of its C-terminal domain (APC-C), which bears cytoskeleton-regulating sequences, correlate with colorectal cancer. The cellular roles of APC in mitosis are widely studied, but the molecular mechanisms of its interaction with the cytoskeleton are poorly understood. Here, we investigated how APC-C regulates microtubule properties, and found that it promotes both microtubule growth and shrinkage. Strikingly, APC-C accumulates at shrinking microtubule extremities, a common characteristic of depolymerases. Cryo-electron microscopy revealed that APC-C adopts an extended conformation along the protofilament crest and showed the presence of ring-like tubulin oligomers around the microtubule wall, which required the presence of two APC-C sub-domains. A mutant of APC-C that was incapable of decorating microtubules with ring-like tubulin oligomers exhibited a reduced effect on microtubule dynamics. Finally, whereas native APC-C rescued defective chromosome alignment in metaphase cells silenced for APC, the ring-incompetent mutant failed to correct mitotic defects. Thus, the bilateral interaction of APC-C with tubulin and microtubules likely contributes to its mitotic functions. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c5c.cif.gz | 4.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8c5c.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8c5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c5c_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 8c5c_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 8c5c_validation.xml.gz | 530.7 KB | Display | |
Data in CIF | 8c5c_validation.cif.gz | 825.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/8c5c ftp://data.pdbj.org/pub/pdb/validation_reports/c5/8c5c | HTTPS FTP |
-Related structure data
Related structure data | 16435MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 52 molecules abcdefghijklmnopqrstuvwxyzNOPQ...
#1: Protein | Mass: 50019.922 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: brain / References: UniProt: A0A452DIL8 #2: Protein | Mass: 50204.445 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: brain / References: UniProt: P81947 |
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-Non-polymers , 4 types, 52 molecules
#3: Chemical | ChemComp-TA1 / #4: Chemical | ChemComp-GDP / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-GTP / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: microtubule / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL | |||||||||||||||||||||||||
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Source (natural) | Organism: Bos taurus (cattle) | |||||||||||||||||||||||||
Buffer solution | pH: 6.75 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 37 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Helical symmerty | Angular rotation/subunit: -27.68 ° / Axial rise/subunit: 9.54 Å / Axial symmetry: C1 | ||||||||||||
3D reconstruction | Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11670 / Details: resolution deduced from unmasked FSC is 7.1 A / Symmetry type: HELICAL |