+Open data
-Basic information
Entry | Database: PDB / ID: 6wsl | |||||||||
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Title | Cryo-EM structure of VASH1-SVBP bound to microtubules | |||||||||
Components |
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Keywords | PROTEIN BINDING / Microtubule / Posttranslational modification / Detyrosination / Vasohibin | |||||||||
Function / homology | Function and homology information regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / netrin receptor binding / Post-chaperonin tubulin folding pathway / axonemal microtubule / dorsal root ganglion development / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / regulation of cellular senescence ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / netrin receptor binding / Post-chaperonin tubulin folding pathway / axonemal microtubule / dorsal root ganglion development / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / regulation of cellular senescence / Carboxyterminal post-translational modifications of tubulin / negative regulation of lymphangiogenesis / organelle transport along microtubule / peptidase activator activity / glial cell differentiation / forebrain morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / neuron projection arborization / cytoskeleton-dependent intracellular transport / cerebellar cortex morphogenesis / Formation of tubulin folding intermediates by CCT/TriC / dentate gyrus development / Gap junction assembly / COPI-independent Golgi-to-ER retrograde traffic / pyramidal neuron differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / Hedgehog 'off' state / Assembly and cell surface presentation of NMDA receptors / centrosome cycle / motor behavior / negative regulation of endothelial cell migration / COPI-dependent Golgi-to-ER retrograde traffic / labyrinthine layer blood vessel development / response to L-glutamate / smoothened signaling pathway / intercellular bridge / regulation of synapse organization / axon development / startle response / negative regulation of endothelial cell proliferation / locomotory exploration behavior / Recycling pathway of L1 / microtubule polymerization / microtubule-based process / negative regulation of blood vessel endothelial cell migration / protein secretion / RHO GTPases activate IQGAPs / response to tumor necrosis factor / regulation of angiogenesis / response to mechanical stimulus / COPI-mediated anterograde transport / metallocarboxypeptidase activity / Activation of AMPK downstream of NMDARs / condensed chromosome / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / homeostasis of number of cells within a tissue / negative regulation of protein ubiquitination / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / cellular response to calcium ion / AURKA Activation by TPX2 / negative regulation of angiogenesis / adult locomotory behavior / filopodium / axon guidance / cell periphery / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / RHO GTPases Activate Formins / peptide binding / neuron migration / synapse organization / visual learning / neuromuscular junction / PKR-mediated signaling / recycling endosome / cerebral cortex development / mitotic spindle / structural constituent of cytoskeleton / memory / microtubule cytoskeleton organization / response to wounding / Aggrephagy / HCMV Early Events / cytoplasmic ribonucleoprotein granule / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / lamellipodium Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Li, F. / Li, Y. / Yu, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2020 Title: Cryo-EM structure of VASH1-SVBP bound to microtubules. Authors: Faxiang Li / Yang Li / Xuecheng Ye / Haishan Gao / Zhubing Shi / Xuelian Luo / Luke M Rice / Hongtao Yu / Abstract: The dynamic tyrosination-detyrosination cycle of α-tubulin regulates microtubule functions. Perturbation of this cycle impairs mitosis, neural physiology, and cardiomyocyte contraction. The ...The dynamic tyrosination-detyrosination cycle of α-tubulin regulates microtubule functions. Perturbation of this cycle impairs mitosis, neural physiology, and cardiomyocyte contraction. The carboxypeptidases vasohibins 1 and 2 (VASH1 and VASH2), in complex with the small vasohibin-binding protein (SVBP), mediate α-tubulin detyrosination. These enzymes detyrosinate microtubules more efficiently than soluble αβ-tubulin heterodimers. The structural basis for this substrate preference is not understood. Using cryo-electron microscopy (cryo-EM), we have determined the structure of human VASH1-SVBP bound to microtubules. The acidic C-terminal tail of α-tubulin binds to a positively charged groove near the active site of VASH1. VASH1 forms multiple additional contacts with the globular domain of α-tubulin, including contacts with a second α-tubulin in an adjacent protofilament. Simultaneous engagement of two protofilaments by VASH1 can only occur within the microtubule lattice, but not with free αβ heterodimers. These lattice-specific interactions enable preferential detyrosination of microtubules by VASH1. | |||||||||
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 | 6wsl.cif.gz | 445 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wsl.ent.gz | 358.2 KB | Display | PDB format |
PDBx/mmJSON format | 6wsl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wsl_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6wsl_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6wsl_validation.xml.gz | 61.7 KB | Display | |
Data in CIF | 6wsl_validation.cif.gz | 93.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/6wsl ftp://data.pdbj.org/pub/pdb/validation_reports/ws/6wsl | HTTPS FTP |
-Related structure data
Related structure data | 21893MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 50188.441 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TUBA1A, TUBA3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q71U36 #2: Protein | Mass: 50481.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TUBB3, TUBB4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13509 #3: Protein | Mass: 29780.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VASH1, KIAA1036, VASH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase #4: Protein | Mass: 7821.939 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SVBP, CCDC23 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N300 |
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-Non-polymers , 2 types, 4 molecules
#5: Chemical | #6: Chemical | |
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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: Tenary complex of microtubule with VASH1-SVBP complex / Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 86 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 |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46999 / Symmetry type: POINT |