7A0O | pdb_00007a0o

NMR structure of flagelliform spidroin (FlagSp) N-terminal domain from Trichonephila clavipes at pH 5.5


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report

Validation slider image for 7A0O

This is version 1.3 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 Biological Chem 298: 101913-101913

  • DOI: https://doi.org/10.1016/j.jbc.2022.101913
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 28.51 kDa 
  • Atom Count: 1,994 
  • Modeled Residue Count: 270 
  • Deposited Residue Count: 270 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Other
  • Version 1.3: 2024-06-19
    Changes: Data collection, Database references