5H7P

NMR structure of the Vta1NTD-Did2(176-204) complex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

NMR studies on the interactions between yeast Vta1 and Did2 during the multivesicular bodies sorting pathway

Shen, J.Yang, Z.Wang, J.Zhao, B.Lan, W.Wang, C.Zhang, X.Wild, C.J.Liu, M.Xu, Z.Cao, C.

(2016) Sci Rep 6: 38710-38710

  • DOI: https://doi.org/10.1038/srep38710
  • Primary Citation of Related Structures:  
    5H7P

  • PubMed Abstract: 

    As an AAA-ATPase, Vps4 is important for function of multivesicular bodies (MVB) sorting pathway, which involves in cellular phenomena ranging from receptor down-regulation to viral budding to cytokinesis. The activity of Vps4 is stimulated by the interactions between Vta1 N-terminus (named as Vta1NTD) and Did2 fragment (176-204 aa) (termed as Did2 176-204 ) or Vps60 (128-186 aa) (termed as Vps60 128-186 ). The structural basis of how Vta1NTD binds to Did2 176-204 is still unclear. To address this, in this report, the structure of Did2 176-204 in complex with Vta1NTD was determined by NMR techniques, demonstrating that Did2 176-204 interacts with Vta1NTD through its helix α6' extending over the 2 nd and the 3 rd α-helices of Vta1NTD microtubule interacting and transport 1 (MIT1) domain. The residues within Did2 176-204 helix α6' in the interface make up of an amino acid sequence as E 192 'xxL 195 'xxR 198 'L 199 'xxL 202 'R 203 ', identical to type 1 MIT-interacting motif (MIM1) (D/E)xxLxxRLxxL(K/R) of CHMP1A 180-196 observed in Vps4-CHMP1A complex structure, indicating that Did2 binds to Vta1NTD through canonical MIM1 interactions. Moreover, the Did2 binding does not result in Vta1NTD significant conformational changes, revealing that Did2, similar to Vps60, enhances Vta1 stimulation of Vps4 ATPase activity in an indirect manner.


  • Organizational Affiliation

    State Key Laboratory of Bioorganic and Natural Products Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein VTA1167Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VTA1YLR181C
UniProt
Find proteins for Q06263 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06263 
Go to UniProtKB:  Q06263
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06263
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein-sorting-associated protein 4629Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DID2CHM1FTI1VPS46YKR035W-A
UniProt
Find proteins for P69771 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P69771 
Go to UniProtKB:  P69771
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69771
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of ChinaChina2011CB966300
Science and Technology Commission of Shanghai MunicipalityChina15ZR1449300

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Data collection, Database references, Other, Structure summary
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references