5LKN | pdb_00005lkn

NMR solution structure of human FNIII domain 2 of NCAM

• PDB DOI: https://doi.org/10.2210/pdb5LKN/pdb
• BMRB: 34026

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-22 Released: 2016-09-14 
• Deposition Author(s): Slapsak, U., Salzano, G., Amin, L., Abskharon, R.N.N., Ilc, G., Zupancic, B., Biljan, I., Plavec, J., Giachin, G., Legname, G.
• Funding Organization(s): Slovenian Research Agency

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Experimental Data Snapshot

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

Literature

The N Terminus of the Prion Protein Mediates Functional Interactions with the Neuronal Cell Adhesion Molecule (NCAM) Fibronectin Domain.

Slapsak, U., Salzano, G., Amin, L., Abskharon, R.N., Ilc, G., Zupancic, B., Biljan, I., Plavec, J., Giachin, G., Legname, G.

(2016) J Biol Chem 291: 21857-21868

• PubMed: 27535221 
• DOI: https://doi.org/10.1074/jbc.M116.743435
• Primary Citation Related Structures: 
  5LKN


• PubMed Abstract: 
  

  The cellular form of the prion protein (PrP ^C ) is a highly conserved glycoprotein mostly expressed in the central and peripheral nervous systems by different cell types in mammals. A misfolded, pathogenic isoform, denoted as prion, is related to a class of neurodegenerative diseases known as transmissible spongiform encephalopathy. PrP ^C function has not been unequivocally clarified, and it is rather defined as a pleiotropic protein likely acting as a dynamic cell surface scaffolding protein for the assembly of different signaling modules. Among the variety of PrP ^C protein interactors, the neuronal cell adhesion molecule (NCAM) has been studied in vivo, but the structural basis of this functional interaction is still a matter of debate. Here we focused on the structural determinants responsible for human PrP ^C (HuPrP) and NCAM interaction using stimulated emission depletion (STED) nanoscopy, SPR, and NMR spectroscopy approaches. PrP ^C co-localizes with NCAM in mouse hippocampal neurons, and this interaction is mainly mediated by the intrinsically disordered PrP ^C N-terminal tail, which binds with high affinity to the NCAM fibronectin type-3 domain. NMR structural investigations revealed surface-interacting epitopes governing the interaction between HuPrP N terminus and the second module of the NCAM fibronectin type-3 domain. Our data provided molecular details about the interaction between HuPrP and the NCAM fibronectin domain, and revealed a new role of PrP ^C N terminus as a dynamic and functional element responsible for protein-protein interaction.

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Organizational Affiliation: 
• From the Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
the Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, Trieste I-34136, Italy.
the Structural Biology Research Center, Vrije Universiteit Brussel, VIB, Pleinlaan 2, 1050, Brussels, Belgium, the National Institute of Oceanography and Fisheries (NIOF), 11516 Cairo, Egypt, and the Van Andel Research Institute, Grand Rapids, Michigan 49503.
From the Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia, the EN-FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia.
the Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, Zagreb HR-10000, Croatia.
From the Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia, the EN-FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia, the Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia, [e-mail].
the Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, Trieste I-34136, Italy, the Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, 38000-Grenoble, France.
the Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, Trieste I-34136, Italy, [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 11.86 kDa 
• Atom Count: 836 
• Modeled Residue Count: 103 
• Deposited Residue Count: 103 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neural cell adhesion molecule 1	A	103	Homo sapiens	Mutation(s): 0  Gene Names: NCAM1, NCAM
UniProt & NIH Common Fund Data Resources
Find proteins for P13591 (Homo sapiens) Explore P13591  Go to UniProtKB:  P13591
PHAROS:  P13591 GTEx:  ENSG00000149294

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Slapsak, U., Salzano, G., Amin, L., Abskharon, R.N.N., Ilc, G., Zupancic, B., Biljan, I., Plavec, J., Giachin, G., Legname, G.

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Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	P1-242

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Database references
• Version 1.2: 2016-10-26
  Changes: Database references
• Version 1.3: 2019-05-08
  Changes: Data collection
• Version 1.4: 2024-06-19
  Changes: Data collection, Database references