5IZ2

Crystal structure of the N. clavipes spidroin NTD at pH 6.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Nephila clavipes Major Ampullate Spidroin 1A N-terminal Domain Reveals Plasticity at the Dimer Interface.

Atkison, J.H.Parnham, S.Marcotte, W.R.Olsen, S.K.

(2016) J.Biol.Chem. 291: 19006-19017

  • DOI: 10.1074/jbc.M116.736710

  • PubMed Abstract: 
  • Spider dragline silk is a natural polymer harboring unique physical and biochemical properties that make it an ideal biomaterial. Artificial silk production requires an understanding of the in vivo mechanisms spiders use to convert soluble proteins, ...

    Spider dragline silk is a natural polymer harboring unique physical and biochemical properties that make it an ideal biomaterial. Artificial silk production requires an understanding of the in vivo mechanisms spiders use to convert soluble proteins, called spidroins, into insoluble fibers. Controlled dimerization of the spidroin N-terminal domain (NTD) is crucial to this process. Here, we report the crystal structure of the Nephila clavipes major ampullate spidroin NTD dimer. Comparison of our N. clavipes NTD structure with previously determined Euprosthenops australis NTD structures reveals subtle conformational alterations that lead to differences in how the subunits are arranged at the dimer interface. We observe a subset of contacts that are specific to each ortholog, as well as a substantial increase in asymmetry in the interactions observed at the N. clavipes NTD dimer interface. These asymmetric interactions include novel intermolecular salt bridges that provide new insights into the mechanism of NTD dimerization. We also observe a unique intramolecular "handshake" interaction between two conserved acidic residues that our data suggest adds an additional layer of complexity to the pH-sensitive relay mechanism for NTD dimerization. The results of a panel of tryptophan fluorescence dimerization assays probing the importance of these interactions support our structural observations. Based on our findings, we propose that conformational selectivity and plasticity at the NTD dimer interface play a role in the pH-dependent transition of the NTD from monomer to stably associated dimer as the spidroin progresses through the silk extrusion duct.


    Organizational Affiliation

    From the Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425 and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major ampullate spidroin 1A
B, A
144Nephila clavipesMutation(s): 0 
Gene Names: MaSp1A
Find proteins for B5SYS5 (Nephila clavipes)
Go to UniProtKB:  B5SYS5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Major ampullate spidroin 1A (Partial C-terminus)
Z
3Nephila clavipesMutation(s): 0 
Gene Names: MaSp1A
Find proteins for B5SYS5 (Nephila clavipes)
Go to UniProtKB:  B5SYS5
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.164 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 67.480α = 90.00
b = 67.480β = 90.00
c = 90.350γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references
  • Version 1.2: 2016-09-14
    Type: Database references