6J7B

Crystal structure of VASH1-SVBP in complex with epoY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Molecular basis of vasohibins-mediated detyrosination and its impact on spindle function and mitosis.

Liao, S.Rajendraprasad, G.Wang, N.Eibes, S.Gao, J.Yu, H.Wu, G.Tu, X.Huang, H.Barisic, M.Xu, C.

(2019) Cell Res 29: 533-547

  • DOI: https://doi.org/10.1038/s41422-019-0187-y
  • Primary Citation of Related Structures:  
    6J7B, 6J8F, 6J8N, 6J91, 6J9H

  • PubMed Abstract: 

    α-Tubulin detyrosination, largely catalyzed by vasohibins, is involved in many microtubule (MT)-related cellular events. In this study, we identified a core heterodimeric complex of human small vasohibin-binding protein (SVBP) and vasohibin 1 (VASH1) (hereafter denoted as SVBP-VASH1) that catalyzes the detyrosination of a peptide derived from C-terminus of α-tubulin. We further solved the crystal structures of the SVBP-VASH1 heterodimer alone and in complex with either an inhibitor or a mutant substrate peptide. Our structural research, complemented by biochemical and mutagenesis experiments, resulted in identification of the key residues for VASH1 binding to SVBP and α-tubulin substrate. Our in vivo experiments reveal that MT detyrosination in general, as well as the interactions between SVBP, VASH1, and α-tubulin, are critical for spindle function and accurate chromosome segregation during mitosis. Furthermore, we found that the phenotypes caused by the depletion of vasohibins were largely rescued upon co-depletion of kinesin13/MCAK, suggesting the coordination between the MT depolymerase and MT detyrosination during mitosis. Thus our work not only provides structural insights into the molecular mechanism of α-tubulin detyrosination catalyzed by SVBP-bound vasohibins, but also uncovers the key role of vasohibins-mediated MT detyrosination in spindle morphology and chromosome segregation during mitosis.


  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulinyl-Tyr carboxypeptidase 1250Homo sapiensMutation(s): 0 
Gene Names: VASH1KIAA1036VASH
EC: 3.4.17.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L8A9 (Homo sapiens)
Explore Q7L8A9 
Go to UniProtKB:  Q7L8A9
PHAROS:  Q7L8A9
GTEx:  ENSG00000071246 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7L8A9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small vasohibin-binding protein52Homo sapiensMutation(s): 0 
Gene Names: SVBPCCDC23
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N300 (Homo sapiens)
Explore Q8N300 
Go to UniProtKB:  Q8N300
PHAROS:  Q8N300
GTEx:  ENSG00000177868 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N300
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BJL
Query on BJL

Download Ideal Coordinates CCD File 
C [auth A]N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine
C15 H19 N O7
NGFYRWHZMJJCIF-NWDGAFQWSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.31α = 90
b = 70.92β = 90
c = 128.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2018YFC1004500
National Natural Science Foundation of ChinaChinathe Thousand Young Talents Program
National Natural Science Foundation of ChinaChinaK18221002

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary