3KYQ

Lipid-induced Conformational Switch Controls Fusion Activity of Longin Domain SNARE Ykt6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.205 

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This is version 1.2 of the entry. See complete history


Literature

Lipid-Induced Conformational Switch Controls Fusion Activity of Longin Domain SNARE Ykt6

Wen, W.Y.Yu, J.Pan, L.F.Wei, Z.Y.Weng, J.W.Wang, W.N.Ong, Y.S.Tran, T.H.T.Hong, W.J.Zhang, M.J.

(2010) Mol Cell 37: 383-395

  • DOI: https://doi.org/10.1016/j.molcel.2010.01.024
  • Primary Citation of Related Structures:  
    3KYQ

  • PubMed Abstract: 

    While most SNAREs are permanently anchored to membranes by their transmembrane domains, the dually lipidated SNARE Ykt6 is found both on intracellular membranes and in the cytosol. The cytosolic Ykt6 is inactive due to the autoinhibition of the SNARE core by its longin domain, although the molecular basis of this inhibition is unknown. Here, we demonstrate that unlipidated Ykt6 adopts multiple conformations, with a small population in the closed state. The structure of Ykt6 in complex with a fatty acid suggests that, upon farnesylation, the Ykt6 SNARE core forms four alpha helices that wrap around the longin domain, forming a dominantly closed conformation. The fatty acid, buried in a hydrophobic groove formed between the longin domain and its SNARE core, is essential for maintaining the autoinhibited conformation of Ykt6. Our study reveals that the posttranslationally attached farnesyl group can actively regulate Ykt6 fusion activity in addition to its anticipated membrane-anchoring role.


  • Organizational Affiliation

    Institutes of Biomedical Sciences, Fudan University, Shanghai, P.R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptobrevin homolog YKT6199Rattus norvegicusMutation(s): 0 
Gene Names: Ykt6
EC: 2.3.1
Membrane Entity: Yes 
UniProt
Find proteins for Q5EGY4 (Rattus norvegicus)
Explore Q5EGY4 
Go to UniProtKB:  Q5EGY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5EGY4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DPV Binding MOAD:  3KYQ Kd: 6.10e+4 (nM) from 1 assay(s)
PDBBind:  3KYQ Kd: 6.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.205 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.81α = 90
b = 59.71β = 90
c = 108.33γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description