2LUH | pdb_00002luh

NMR structure of the Vta1-Vps60 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

Validation slider image for 2LUH

This is version 1.4 of the entry. See complete history

Literature

Structural Basis of Molecular Recognition between ESCRT-III-like Protein Vps60 and AAA-ATPase Regulator Vta1 in the Multivesicular Body Pathway.

Yang, Z.Vild, C.Ju, J.Zhang, X.Liu, J.Shen, J.Zhao, B.Lan, W.Gong, F.Liu, M.Cao, C.Xu, Z.

(2012) J Biological Chem 287: 43899-43908

  • DOI: https://doi.org/10.1074/jbc.M112.390724
  • Primary Citation Related Structures: 
    2LUH

  • PubMed Abstract: 

    The AAA-ATPase Vps4 is critical for function of the multivesicular body sorting pathway, which impacts cellular phenomena ranging from receptor down-regulation to viral budding to cytokinesis. Vps4 activity is stimulated by the interaction between Vta1 and Vps60, but the structural basis for this interaction is unclear. The fragment Vps60(128-186) was reported to display the full activity of Vps60. Vta1 interacts with Vps60 using its N-terminal domain (Vta1NTD). In this work, the structure of Vps60(128-186) in complex with Vta1NTD was determined using NMR techniques, demonstrating a novel recognition mode of the microtubule-interacting and transport (MIT) domain in which Vps60(128-186) interacts with Vta1NTD through helices α4' and α5', extending over Vta1NTD MIT2 domain helices 1-3. The Vps60 binding does not result in Vta1 conformational changes, further revealing the fact that Vps4 ATPase is enhanced by the interaction between Vta1 and Vps60 in an unanticipated manner.


  • Organizational Affiliation
    • State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.

Macromolecule Content 

  • Total Structure Weight: 25.67 kDa 
  • Atom Count: 1,793 
  • Modeled Residue Count: 226 
  • Deposited Residue Count: 226 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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
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UniProt GroupQ06263
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar protein-sorting-associated protein 6059Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPS60CHM5MOS10YDR486C
UniProt
Find proteins for Q03390 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03390 
Go to UniProtKB:  Q03390
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03390
Sequence Annotations
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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 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2012-11-14
    Changes: Database references
  • Version 1.2: 2013-01-09
    Changes: Database references
  • Version 1.3: 2023-06-14
    Changes: Data collection, Database references, Other
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references