8GS7 | pdb_00008gs7

SOLUTION NMR STRUCTURE OF N-TERMINAL DOMAIN OF TRICONEPHILA CLAVIPES MAJOR AMPULLATE SPIDROIN 2

• PDB DOI: https://doi.org/10.2210/pdb8GS7/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Trichonephila clavipes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-05 Released: 2023-03-15 
• Deposition Author(s): Oktaviani, N.A., Malay, A.D., Matsugami, A., Hayashi, F., Numata, K.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

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

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

• PubMed: 36990448 
• DOI: https://doi.org/10.1021/acs.biomac.2c01344
• Primary Citation 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.

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Organizational Affiliation: 
• Biomacromolecules Research Team, RIKEN Center for the Sustainable Resource Sciences, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigaku, Katsura, Kyoto 615-8510, Japan.
Institute for Advanced Bioscience, Keio University, 403-1 Nihonkoku, Daihouji, Tsuruoka, Yamagata 997-0017, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 14.47 kDa 
• Atom Count: 1,004 
• Modeled Residue Count: 138 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major ampullate spidroin 2 variant 3	A	138	Trichonephila clavipes	Mutation(s): 0  Gene Names: MaSp2
UniProt
Find proteins for A0A8X6WH47 (Trichonephila clavipes) Explore A0A8X6WH47  Go to UniProtKB:  A0A8X6WH47

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-15 
Deposition Author(s): Oktaviani, N.A., Malay, A.D., Matsugami, A., Hayashi, F., Numata, K.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJER1602
Japan Science and Technology	Japan	Impulsing paradigm through disruptive technology program

Revision History  

• 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