7OOM

N-terminal domain of FlSp spidroin from Nephila clavipes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The dimerization mechanism of the N-terminal domain of spider silk proteins is conserved despite extensive sequence divergence.

Sarr, M.Kitoka, K.Walsh-White, K.A.Kaldmae, M.Metlans, R.Tars, K.Mantese, A.Shah, D.Landreh, M.Rising, A.Johansson, J.Jaudzems, K.Kronqvist, N.

(2022) J Biol Chem 298: 101913-101913

  • DOI: https://doi.org/10.1016/j.jbc.2022.101913
  • Primary Citation of Related Structures:  
    7A0I, 7A0O, 7OOM

  • PubMed Abstract: 

    The N-terminal (NT) domain of spider silk proteins (spidroins) is crucial for their storage at high concentrations and also regulates silk assembly. NTs from the major ampullate spidroin (MaSp) and the minor ampullate spidroin are monomeric at neutral pH and confer solubility to spidroins, whereas at lower pH, they dimerize to interconnect spidroins in a fiber. This dimerization is known to result from modulation of electrostatic interactions by protonation of well-conserved glutamates, although it is undetermined if this mechanism applies to other spidroin types as well. Here, we determine the solution and crystal structures of the flagelliform spidroin NT, which shares only 35% identity with MaSp NT, and investigate the mechanisms of its dimerization. We show that flagelliform spidroin NT is structurally similar to MaSp NT and that the electrostatic intermolecular interaction between Asp 40 and Lys 65 residues is conserved. However, the protonation events involve a different set of residues than in MaSp, indicating that an overall mechanism of pH-dependent dimerization is conserved but can be mediated by different pathways in different silk types.


  • Organizational Affiliation

    Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flagelliform spidroin variant 1
A, B
135Trichonephila clavipesMutation(s): 0 
Gene Names: Flag
UniProt
Find proteins for A0A2S2B4P9 (Trichonephila clavipes)
Explore A0A2S2B4P9 
Go to UniProtKB:  A0A2S2B4P9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2S2B4P9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.878α = 90
b = 58.89β = 106.65
c = 46.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
SHELXCDphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Regional Development FundLatvia1.1.1.1/18/A/004

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references