Biological Assembly 1  

 3D View: Structure

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21061.40 
• Atom Count: 1428 
• Residue Count: 196 
• Unique protein chains: 1

2N97

DD homodimer

• DOI: 10.2210/pdb2N97/pdb
• BMRB: 25883

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2015-11-07 Released: 2015-12-23 
• Deposition Author(s): Lin, Z., Ibanez, C.F.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structural basis of death domain signaling in the p75 neurotrophin receptor

Lin, Z., Tann, J.Y., Goh, E.T., Kelly, C., Lim, K.B., Gao, J.F., Ibanez, C.F.

(2015) Elife 4: 11692-11692

• PubMed: 26646181 
• DOI: 10.7554/eLife.11692
• Primary Citation of Related Structures:  
  2N83, 2N80, 2N7Z


• PubMed Abstract: 
  

Death domains (DDs) mediate assembly of oligomeric complexes for activation of downstream signaling pathways through incompletely understood mechanisms. Here we report structures of complexes formed by the DD of p75 neurotrophin receptor (p75(NTR)) with RhoGDI, for activation of the RhoA pathway, with caspase recruitment domain (CARD) of RIP2 kinase, for activation of the NF-kB pathway, and with itself, revealing how DD dimerization controls access of intracellular effectors to the receptor. RIP2 CARD and RhoGDI bind to p75(NTR) DD at partially overlapping epitopes with over 100-fold difference in affinity, revealing the mechanism by which RIP2 recruitment displaces RhoGDI upon ligand binding. The p75(NTR) DD forms non-covalent, low-affinity symmetric dimers in solution. The dimer interface overlaps with RIP2 CARD but not RhoGDI binding sites, supporting a model of receptor activation triggered by separation of DDs. These structures reveal how competitive protein-protein interactions orchestrate the hierarchical activation of downstream pathways in non-catalytic receptors.

---

Organizational Affiliation: 

Department of Physiology, National University of Singapore, Singapore, Singapore.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Tumor necrosis factor receptor superfamily member 16	A, B	98	Homo sapiens	Mutation(s): 0  Gene Names: NGFR (TNFRSF16)
Find proteins for P08138 (Homo sapiens) Go to Gene View: NGFR Go to UniProtKB:  P08138

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-11-07 
• Released Date: 2015-12-23 
• Deposition Author(s): Lin, Z., Ibanez, C.F.

Revision History 

• Version 1.0: 2015-12-23
  Type: Initial release
• Version 1.1: 2016-04-27
  Type: Structure summary