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- PDB-6wsl: Cryo-EM structure of VASH1-SVBP bound to microtubules -

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Basic information

Entry
Database: PDB / ID: 6wsl
TitleCryo-EM structure of VASH1-SVBP bound to microtubules
Components
  • Small vasohibin-binding protein
  • Tubulin alpha-1A chain
  • Tubulin beta-3 chain
  • Tubulinyl-Tyr carboxypeptidase 1
KeywordsPROTEIN 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 / dorsal root ganglion development / Post-chaperonin tubulin folding pathway / axonemal microtubule / negative regulation of lymphangiogenesis / Cilium Assembly / regulation of cellular senescence ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / netrin receptor binding / dorsal root ganglion development / Post-chaperonin tubulin folding pathway / axonemal microtubule / negative regulation of lymphangiogenesis / Cilium Assembly / regulation of cellular senescence / cytoskeleton-dependent intracellular transport / organelle transport along microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Carboxyterminal post-translational modifications of tubulin / forebrain morphogenesis / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / cerebellar cortex morphogenesis / glial cell differentiation / dentate gyrus development / Formation of tubulin folding intermediates by CCT/TriC / neuron projection arborization / flagellated sperm motility / Gap junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / COPI-independent Golgi-to-ER retrograde traffic / Assembly and cell surface presentation of NMDA receptors / response to L-glutamate / pyramidal neuron differentiation / centrosome cycle / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / peptidase activator activity / COPI-dependent Golgi-to-ER retrograde traffic / smoothened signaling pathway / regulation of synapse organization / axon development / negative regulation of endothelial cell proliferation / startle response / motor behavior / response to tumor necrosis factor / Recycling pathway of L1 / locomotory exploration behavior / microtubule polymerization / negative regulation of blood vessel endothelial cell migration / protein secretion / regulation of angiogenesis / sperm flagellum / response to mechanical stimulus / RHO GTPases activate IQGAPs / microtubule-based process / Hedgehog 'off' state / intercellular bridge / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / condensed chromosome / metallocarboxypeptidase activity / negative regulation of protein ubiquitination / 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 / peptide binding / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / homeostasis of number of cells within a tissue / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / axon guidance / cellular response to calcium ion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / negative regulation of angiogenesis / AURKA Activation by TPX2 / adult locomotory behavior / cell periphery / Translocation of SLC2A4 (GLUT4) to the plasma membrane / filopodium / neuromuscular junction / intracellular protein transport / RHO GTPases Activate Formins / synapse organization / recycling endosome / cerebral cortex development / PKR-mediated signaling / visual learning / structural constituent of cytoskeleton / response to wounding / microtubule cytoskeleton organization / memory / cytoplasmic ribonucleoprotein granule / neuron migration / apical part of cell / HCMV Early Events / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / mitotic spindle / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition
Similarity search - Function
Tubulinyl-Tyr carboxypeptidase / Small vasohibin-binding protein / Vasohibin / Coiled-coil domain-containing protein 23 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal ...Tubulinyl-Tyr carboxypeptidase / Small vasohibin-binding protein / Vasohibin / Coiled-coil domain-containing protein 23 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta-3 chain / Tubulin alpha-1A chain / Tubulinyl-Tyr carboxypeptidase 1 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLi, F. / Li, Y. / Yu, H.
Funding support United States, 2items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP160667-P2 United States
Welch FoundationI-1441 United States
CitationJournal: 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
DepositionMay 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Tubulin alpha-1A chain
B: Tubulin beta-3 chain
C: Tubulinyl-Tyr carboxypeptidase 1
D: Small vasohibin-binding protein
E: Tubulin alpha-1A chain
F: Tubulin beta-3 chain
G: Tubulinyl-Tyr carboxypeptidase 1
H: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,63312
Polymers276,5458
Non-polymers2,0894
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Tubulin alpha-1A chain / Alpha-tubulin 3 / Tubulin B-alpha-1 / Tubulin alpha-3 chain


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 Tubulin beta-3 chain / Tubulin beta-4 chain / Tubulin beta-III


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 Tubulinyl-Tyr carboxypeptidase 1 / Tubulin carboxypeptidase 1 / Tyrosine carboxypeptidase 1 / TTCP 1 / Vasohibin-1


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 Small vasohibin-binding protein / Coiled coil domain-containing protein 23


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 ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-CPP, energy-carrying molecule analogue*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tenary complex of microtubule with VASH1-SVBP complex / Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 86 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46999 / Symmetry type: POINT

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