Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 33.99 kDa 
• Atom Count: 2185 
• Residue Count: 261 
• Unique protein chains: 3

6J8F

Crystal structure of SVBP-VASH1 with peptide mimic the C-terminal of alpha-tubulin

• DOI: 10.2210/pdb6J8F/pdb

• Classification: PEPTIDE BINDING PROTEIN/HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG, Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-18 Released: 2019-06-19 
• Deposition Author(s): Liao, S., Gao, J., Xu, C., Structural Genomics Consortium (SGC)
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.237 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

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

• PubMed: 31171830 
• DOI: 10.1038/s41422-019-0187-y
• Primary Citation of Related Structures:  
  6J7B, 6J8N, 6J91, 6J8F, 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.

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Organizational Affiliation: 

Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Small vasohibin-binding protein	A	46	Homo sapiens	Mutation(s): 0  Gene Names: SVBP, CCDC23
Find proteins for Q8N300 (Homo sapiens) Explore Q8N300  Go to UniProtKB:  Q8N300
NIH Common Fund Data Resources
PHAROS:  Q8N300 GTEx:  ENSG00000177868

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulinyl-Tyr carboxypeptidase 1	B	238	Homo sapiens	Mutation(s): 0  Gene Names: VASH1, KIAA1036, VASH EC: 3.4.17.17
Find proteins for Q7L8A9 (Homo sapiens) Explore Q7L8A9  Go to UniProtKB:  Q7L8A9
NIH Common Fund Data Resources
PHAROS:  Q7L8A9 GTEx:  ENSG00000071246

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
8-mer peptide	C	8	Homo sapiens	Mutation(s): 0  Gene Names: TUBA1A, TUBA3
Find proteins for Q71U36 (Homo sapiens) Explore Q71U36  Go to UniProtKB:  Q71U36
NIH Common Fund Data Resources
PHAROS:  Q71U36 GTEx:  ENSG00000167552

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.237 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.95	α = 90
b = 108.377	β = 90
c = 46.896	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-01-18 
• Released Date: 2019-06-19 
Deposition Author(s): Liao, S., Gao, J., Xu, C., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31500601
National Natural Science Foundation of China	China	31570737
National Natural Science Foundation of China	China	31770806

Revision History 

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Database references