2LTH | pdb_00002lth

NMR structure of major ampullate spidroin 1 N-terminal domain at pH 5.5

• PDB DOI: https://doi.org/10.2210/pdb2LTH/pdb
• BMRB: 18480

• Classification: STRUCTURAL PROTEIN
• Organism(s): Euprosthenops australis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-05-25 Released: 2013-11-27 
• Deposition Author(s): Otikovs, M., Jaudzems, K., Nordling, K., Landreh, M., Rising, A., Askarieh, G., Knight, S., Johansson, J.

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Experimental Data Snapshot

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

Literature

Sequential pH-driven dimerization and stabilization of the N-terminal domain enables rapid spider silk formation.

Kronqvist, N., Otikovs, M., Chmyrov, V., Chen, G., Andersson, M., Nordling, K., Landreh, M., Sarr, M., Jornvall, H., Wennmalm, S., Widengren, J., Meng, Q., Rising, A., Otzen, D., Knight, S.D., Jaudzems, K., Johansson, J.

(2014) Nat Commun 5: 3254-3254

• PubMed: 24510122 
• DOI: https://doi.org/10.1038/ncomms4254
• Primary Citation Related Structures: 
  2LTH


• PubMed Abstract: 
  

  The mechanisms controlling the conversion of spider silk proteins into insoluble fibres, which happens in a fraction of a second and in a defined region of the silk glands, are still unresolved. The N-terminal domain changes conformation and forms a homodimer when pH is lowered from 7 to 6; however, the molecular details still remain to be determined. Here we investigate site-directed mutants of the N-terminal domain from Euprosthenops australis major ampullate spidroin 1 and find that the charged residues D40, R60 and K65 mediate intersubunit electrostatic interactions. Protonation of E79 and E119 is required for structural conversions of the subunits into a dimer conformation, and subsequent protonation of E84 around pH 5.7 leads to the formation of a fully stable dimer. These residues are highly conserved, indicating that the now proposed three-step mechanism prevents premature aggregation of spidroins and enables fast formation of spider silk fibres in general.

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Organizational Affiliation: 
• KI Alzheimer Disease Research Centre, NVS Department, Karolinska Institutet, Novum, 5th floor, SE-141 86 Stockholm, Sweden.
Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia.
Experimental Biomolecular Physics, Royal Institute of Technology-KTH, Albanova, SE-106 91 Stockholm, Sweden.
Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai CN-201620, China.
Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, The Biomedical Centre, SE-751 23 Uppsala, Sweden.
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
1] Experimental Biomolecular Physics, Royal Institute of Technology-KTH, Albanova, SE-106 91 Stockholm, Sweden [2] Science for Life Laboratory, SE-171 65 Solna, Sweden.
1] KI Alzheimer Disease Research Centre, NVS Department, Karolinska Institutet, Novum, 5th floor, SE-141 86 Stockholm, Sweden [2] Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, The Biomedical Centre, SE-751 23 Uppsala, Sweden.
Center for Insoluble Protein Structures (inSPIN), iNANO and Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden.
1] KI Alzheimer Disease Research Centre, NVS Department, Karolinska Institutet, Novum, 5th floor, SE-141 86 Stockholm, Sweden [2] Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, The Biomedical Centre, SE-751 23 Uppsala, Sweden [3] Institute of Mathematics and Natural Sciences, Tallinn University, Narva mnt 25, EE-101 20 Tallinn, Estonia.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.37 kDa 
• Atom Count: 1,972 
• Modeled Residue Count: 274 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major ampullate spidroin 1	A, B	137	Euprosthenops australis	Mutation(s): 0  Gene Names: MaSp1
UniProt
Find proteins for Q05H60 (Euprosthenops australis) Explore Q05H60  Go to UniProtKB:  Q05H60

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-27 
Deposition Author(s): Otikovs, M., Jaudzems, K., Nordling, K., Landreh, M., Rising, A., Askarieh, G., Knight, S., Johansson, J.

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2014-03-26
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references