2IFU

Crystal Structure of a Gamma-SNAP from Danio rerio


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and dynamics of gamma-SNAP: insight into flexibility of proteins from the SNAP family.

Bitto, E.Bingman, C.A.Kondrashov, D.A.McCoy, J.G.Bannen, R.M.Wesenberg, G.E.Phillips, G.N.

(2008) Proteins 70: 93-104

  • DOI: 10.1002/prot.21468
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Soluble N-ethylmaleimide-sensitive factor attachment protein gamma (gamma-SNAP) is a member of an eukaryotic protein family involved in intracellular membrane trafficking. The X-ray structure of Brachydanio rerio gamma-SNAP was determined to 2.6 A an ...

    Soluble N-ethylmaleimide-sensitive factor attachment protein gamma (gamma-SNAP) is a member of an eukaryotic protein family involved in intracellular membrane trafficking. The X-ray structure of Brachydanio rerio gamma-SNAP was determined to 2.6 A and revealed an all-helical protein comprised of an extended twisted-sheet of helical hairpins with a helical-bundle domain on its carboxy-terminal end. Structural and conformational differences between multiple observed gamma-SNAP molecules and Sec17, a SNAP family protein from yeast, are analyzed. Conformational variation in gamma-SNAP molecules is matched with great precision by the two lowest frequency normal modes of the structure. Comparison of the lowest-frequency modes from gamma-SNAP and Sec17 indicated that the structures share preferred directions of flexibility, corresponding to bending and twisting of the twisted sheet motif. We discuss possible consequences related to the flexibility of the SNAP proteins for the mechanism of the 20S complex disassembly during the SNAP receptors recycling.


    Organizational Affiliation

    Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
gamma-snapA, B, C, D307Danio rerioMutation(s): 10 
Gene Names: zgc:110177napganapgl
Find proteins for Q5BJK3 (Danio rerio)
Explore Q5BJK3 
Go to UniProtKB:  Q5BJK3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.378α = 90
b = 90.813β = 90
c = 264.173γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-10
    Type: Initial release
  • Version 1.1: 2008-01-15
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description