6WSL

Cryo-EM structure of VASH1-SVBP bound to microtubules

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM structure of VASH1-SVBP bound to microtubules.

Li, F., Li, Y., Ye, X., Gao, H., Shi, Z., Luo, X., Rice, L.M., Yu, H.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.58157
  • Primary Citation of Related Structures:  
    6WSL

  • PubMed Abstract: 

    • 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 ...

    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.

    Organizational Affiliation: 

    Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1A chain
A, E
451Homo sapiensMutation(s): 0 
Gene Names: TUBA1A, TUBA3
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Find proteins for Q71U36 (Homo sapiens)
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Go to UniProtKB:  Q71U36
PHAROS:  Q71U36
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UniProt GroupQ71U36
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta-3 chain
B, F
450Homo sapiensMutation(s): 0 
Gene Names: TUBB3, TUBB4
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Find proteins for Q13509 (Homo sapiens)
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PHAROS:  Q13509
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UniProt GroupQ13509
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulinyl-Tyr carboxypeptidase 1
C, G
259Homo sapiensMutation(s): 0 
Gene Names: VASH1, KIAA1036, VASH
EC: 3.4.17.17
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Find proteins for Q7L8A9 (Homo sapiens)
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PHAROS:  Q7L8A9
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UniProt GroupQ7L8A9
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Small vasohibin-binding protein
D, H
66Homo sapiensMutation(s): 0 
Gene Names: SVBP, CCDC23
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Find proteins for Q8N300 (Homo sapiens)
Explore Q8N300 
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PHAROS:  Q8N300
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UniProt GroupQ8N300
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
I [auth A],
K [auth E]		GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
G2P
Query on G2P
Download Ideal Coordinates CCD File 
J [auth B],
L [auth F]		PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
GXTIEXDFEKYVGY-KQYNXXCUSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP160667-P2
Welch FoundationUnited StatesI-1441

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release