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Yorodumi- PDB-7zcw: Cryo-EM structure of GMPCPP-microtubules in complex with VASH2-SVBP -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zcw | ||||||
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Title | Cryo-EM structure of GMPCPP-microtubules in complex with VASH2-SVBP | ||||||
Components |
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Keywords | PROTEIN BINDING / Microtubule / Enzyme / Complex / Detyrosination | ||||||
Function / homology | Function and homology information cell-cell fusion / regulation of metallopeptidase activity / syncytium formation by plasma membrane fusion / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / peptidase activator activity ...cell-cell fusion / regulation of metallopeptidase activity / syncytium formation by plasma membrane fusion / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / peptidase activator activity / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / cytoskeleton-dependent intracellular transport / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / embryonic brain development / COPI-independent Golgi-to-ER retrograde traffic / Prefoldin mediated transfer of substrate to CCT/TriC / Assembly and cell surface presentation of NMDA receptors / Kinesins / positive regulation of axon guidance / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / COPI-dependent Golgi-to-ER retrograde traffic / intercellular bridge / axon development / cytoplasmic microtubule / Recycling pathway of L1 / microtubule-based process / RHOH GTPase cycle / protein secretion / RHO GTPases activate IQGAPs / cellular response to interleukin-4 / regulation of angiogenesis / Hedgehog 'off' state / COPI-mediated anterograde transport / metallocarboxypeptidase activity / Activation of AMPK downstream of NMDARs / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of protein ubiquitination / Recruitment of NuMA to mitotic centrosomes / positive regulation of endothelial cell proliferation / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / neuron migration / modulation of chemical synaptic transmission / PKR-mediated signaling / Schaffer collateral - CA1 synapse / structural constituent of cytoskeleton / mitotic spindle / cerebral cortex development / microtubule cytoskeleton organization / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / positive regulation of angiogenesis / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / double-stranded RNA binding / apical part of cell / mitotic cell cycle / actin binding / microtubule binding / microtubule / cytoskeleton / protein heterodimerization activity / cell division / GTPase activity / ubiquitin protein ligase binding / GTP binding / structural molecule activity / proteolysis / extracellular region / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Choi, S.R. / Blum, T. / Steinmetz, M.O. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: J Cell Biol / Year: 2023 Title: VASH1-SVBP and VASH2-SVBP generate different detyrosination profiles on microtubules. Authors: Sacnicte Ramirez-Rios / Sung Ryul Choi / Chadni Sanyal / Thorsten B Blum / Christophe Bosc / Fatma Krichen / Eric Denarier / Jean-Marc Soleilhac / Béatrice Blot / Carsten Janke / Virginie ...Authors: Sacnicte Ramirez-Rios / Sung Ryul Choi / Chadni Sanyal / Thorsten B Blum / Christophe Bosc / Fatma Krichen / Eric Denarier / Jean-Marc Soleilhac / Béatrice Blot / Carsten Janke / Virginie Stoppin-Mellet / Maria M Magiera / Isabelle Arnal / Michel O Steinmetz / Marie-Jo Moutin / Abstract: The detyrosination/tyrosination cycle of α-tubulin is critical for proper cell functioning. VASH1-SVBP and VASH2-SVBP are ubiquitous enzymes involved in microtubule detyrosination, whose mode of ...The detyrosination/tyrosination cycle of α-tubulin is critical for proper cell functioning. VASH1-SVBP and VASH2-SVBP are ubiquitous enzymes involved in microtubule detyrosination, whose mode of action is little known. Here, we show in reconstituted systems and cells that VASH1-SVBP and VASH2-SVBP drive the global and local detyrosination of microtubules, respectively. We solved the cryo-electron microscopy structure of VASH2-SVBP bound to microtubules, revealing a different microtubule-binding configuration of its central catalytic region compared to VASH1-SVBP. We show that the divergent mode of detyrosination between the two enzymes is correlated with the microtubule-binding properties of their disordered N- and C-terminal regions. Specifically, the N-terminal region is responsible for a significantly longer residence time of VASH2-SVBP on microtubules compared to VASH1-SVBP. We suggest that this VASH region is critical for microtubule detachment and diffusion of VASH-SVBP enzymes on lattices. Our results suggest a mechanism by which VASH1-SVBP and VASH2-SVBP could generate distinct microtubule subpopulations and confined areas of detyrosinated lattices to drive various microtubule-based cellular functions. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zcw.cif.gz | 937.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zcw.ent.gz | 779.3 KB | Display | PDB format |
PDBx/mmJSON format | 7zcw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/7zcw ftp://data.pdbj.org/pub/pdb/validation_reports/zc/7zcw | HTTPS FTP |
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-Related structure data
Related structure data | 14634MC 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 , 4 types, 8 molecules AEBFGHCD
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: P68363 #2: Protein | Mass: 49907.770 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q9BVA1 #3: Protein | | Mass: 40488.914 Da / Num. of mol.: 1 / Mutation: C158A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VASH2, VASHL / Production host: Escherichia coli (E. coli) / References: UniProt: Q86V25, tubulinyl-Tyr carboxypeptidase #4: Protein | | Mass: 8780.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Recombinant C-terminal his6-tag / Source: (gene. exp.) Homo sapiens (human) / Gene: SVBP, CCDC23 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N300 |
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-Non-polymers , 3 types, 12 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-G2P / |
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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: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: VASH2-SVBP complex bound to the microtubule / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.38 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Mixture of VASH2-SVBP and microtubules | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
-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 / Nominal defocus max: 2200 nm / Nominal defocus min: 600 nm |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 1.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3345 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 153041 | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96922 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 54.76 / Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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