2MX9 | pdb_00002mx9

NMR structure of N-terminal domain from A. ventricosus minor ampullate spidroin (MiSp) at pH 5.5

• PDB DOI: https://doi.org/10.2210/pdb2MX9/pdb
• BMRB: 25398

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


• Deposited: 2014-12-17 Released: 2015-08-19 
• Deposition Author(s): Otikovs, M., Jaudzems, K., Chen, G., Nordling, K., Rising, A., Johansson, J.

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Experimental Data Snapshot

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

Literature

Diversified Structural Basis of a Conserved Molecular Mechanism for pH-Dependent Dimerization in Spider Silk N-Terminal Domains.

Otikovs, M., Chen, G., Nordling, K., Landreh, M., Meng, Q., Jornvall, H., Kronqvist, N., Rising, A., Johansson, J., Jaudzems, K.

(2015) Chembiochem 16: 1720-1724

• PubMed: 26033527 
• DOI: https://doi.org/10.1002/cbic.201500263
• Primary Citation Related Structures: 
  2MX8, 2MX9


• PubMed Abstract: 
  

  Conversion of spider silk proteins from soluble dope to insoluble fibers involves pH-dependent dimerization of the N-terminal domain (NT). This conversion is tightly regulated to prevent premature precipitation and enable rapid silk formation at the end of the duct. Three glutamic acid residues that mediate this process in the NT from Euprosthenops australis major ampullate spidroin 1 are well conserved among spidroins. However, NTs of minor ampullate spidroins from several species, including Araneus ventricosus ((Av)MiSp NT), lack one of the glutamic acids. Here we investigate the pH-dependent structural changes of (Av)MiSp NT, revealing that it uses the same mechanism but involves a non-conserved glutamic acid residue instead. Homology modeling of the structures of other MiSp NTs suggests that these harbor different compensatory residues. This indicates that, despite sequence variations, the molecular mechanism underlying pH-dependent dimerization of NT is conserved among different silk types.

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Organizational Affiliation: 
• Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga (Latvia).
Department of Neurobiology, Care Sciences and Society (NVS), Center for Alzheimer Research, Karolinska Institutet, Novum, 141 57 Huddinge (Sweden).
Institute of Biological Sciences and Biotechnology, Donghua University, 201620 Shanghai (China).
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm (Sweden).
Present address: Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY (UK).
Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, The Biomedical Centre, Box 575, 751 23 Uppsala (Sweden).
Department of Neurobiology, Care Sciences and Society (NVS), Center for Alzheimer Research, Karolinska Institutet, Novum, 141 57 Huddinge (Sweden). [e-mail].
Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, The Biomedical Centre, Box 575, 751 23 Uppsala (Sweden). [e-mail].
Institute of Mathematics and Natural Sciences, Tallinn University, Narva mnt 25, 101 20 Tallinn (Estonia). [e-mail].
Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga (Latvia). [e-mail].

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: 28.14 kDa 
• Atom Count: 1,936 
• Modeled Residue Count: 266 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Minor ampullate spidroin	A, B	133	Araneus ventricosus	Mutation(s): 0
UniProt
Find proteins for K4MTL7 (Araneus ventricosus) Explore K4MTL7  Go to UniProtKB:  K4MTL7

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: 2015-08-19 
Deposition Author(s): Otikovs, M., Jaudzems, K., Chen, G., Nordling, K., Rising, A., Johansson, J.

Revision History  

• Version 1.0: 2015-08-19
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary