7WIO

NMR structure of N-terminal domain of Triconephila clavipes of major ampullate spidroin 1


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Unusual p K a Values Mediate the Self-Assembly of Spider Dragline Silk Proteins.

Oktaviani, N.A.Malay, A.D.Matsugami, A.Hayashi, F.Numata, K.

(2023) Biomacromolecules 24: 1604-1616

  • DOI: https://doi.org/10.1021/acs.biomac.2c01344
  • Primary Citation of Related Structures:  
    7WIO, 8GS7

  • PubMed Abstract: 

    Spider dragline silk is a remarkably tough biomaterial and composed primarily of spidroins MaSp1 and MaSp2. During fiber self-assembly, the spidroin N-terminal domains (NTDs) undergo rapid dimerization in response to a pH gradient. However, obtaining a detailed understanding of this mechanism has been hampered by a lack of direct evidence regarding the protonation states of key ionic residues. Here, we elucidated the solution structures of MaSp1 and MaSp2 NTDs from Trichonephila clavipes and determined the experimental p K a values of conserved residues involved in dimerization using NMR. Surprisingly, we found that the Asp40 located on an acidic cluster protonates at an unusually high pH (∼6.5-7.1), suggesting the first step in the pH response. Then, protonation of Glu119 and Glu79 follows, with p K a s above their intrinsic values, contributing toward stable dimer formation. We propose that exploiting the atypical p K a values is a strategy to achieve tight spatiotemporal control of spider silk self-assembly.


  • Organizational Affiliation

    Biomacromolecules Research Team, RIKEN Center for the Sustainable Resource Sciences, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major ampullate spidroin 1A137Trichonephila clavipesMutation(s): 0 
Gene Names: MaSp1A
UniProt
Find proteins for B5SYS5 (Trichonephila clavipes)
Explore B5SYS5 
Go to UniProtKB:  B5SYS5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5SYS5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJER1602
Japan Science and TechnologyJapanImpulsing Paradigm Change through Disrupt Technologies Program (ImPACT)

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2023-04-26
    Changes: Database references
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references