Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.55 kDa 
• Atom Count: 1154 
• Modelled Residue Count: 146 
• Deposited Residue Count: 146 
• Unique protein chains: 2

1DDM

SOLUTION STRUCTURE OF THE NUMB PTB DOMAIN COMPLEXED TO A NAK PEPTIDE

• PDB DOI: 10.2210/pdb1DDM/pdb
• BMRB: 4263

• Classification: SIGNALING PROTEIN/TRANSFERASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-11-11 Released: 2000-04-10 
• Deposition Author(s): Zwahlen, C., Li, S.C., Kay, L.E., Pawson, T., Forman-Kay, J.D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 150 
• Conformers Submitted: 20 
• Selection Criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY 

Literature

Multiple modes of peptide recognition by the PTB domain of the cell fate determinant Numb.

Zwahlen, C., Li, S.C., Kay, L.E., Pawson, T., Forman-Kay, J.D.

(2000) EMBO J 19: 1505-1515

• PubMed: 10747019 
• DOI: 10.1093/emboj/19.7.1505
• Primary Citation of Related Structures:  
  1DDM


• PubMed Abstract: 
  

The phosphotyrosine-binding (PTB) domain of the cell fate determinant Numb is involved in the formation of multiple protein complexes in vivo and can bind a diverse array of peptide sequences in vitro. To investigate the structural basis for the promiscuous nature of this protein module, we have determined its solution structure by NMR in a complex with a peptide containing an NMSF sequence derived from the Numb-associated kinase (Nak). The Nak peptide was found to adopt a significantly different structure from that of a GPpY sequence-containing peptide previously determined. In contrast to the helical turn adopted by the GPpY peptide, the Nak peptide forms a beta-turn at the NMSF site followed by another turn near the C-terminus. The Numb PTB domain appears to recognize peptides that differ in both primary and secondary structures by engaging various amounts of the binding surface of the protein. Our results suggest a mechanism through which a single PTB domain might interact with multiple distinct target proteins to control a complex biological process such as asymmetric cell division.

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Related Citations: 

• Structure of a Numb PTB Domain-Peptide Complex Suggests a Basis for Diverse Binding Specificity
  Li, S.C., Zwahlen, C., Vincent, S.J., McGlade, C.J., Kay, L.E., Pawson, T., Forman-Kay, J.D.
  (1998) Nat Struct Biol 5: 1075

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Organizational Affiliation: 

Structural Biology and Biochemistry Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUMB PROTEIN	A	135	Drosophila melanogaster	Mutation(s): 0  Gene Names: numb, CG3779
UniProt
Find proteins for P16554 (Drosophila melanogaster) Explore P16554  Go to UniProtKB:  P16554

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NUMB ASSOCIATE KINASE	B	11	Drosophila melanogaster	Mutation(s): 0  EC: 2.7.1.37

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 150 
• Conformers Submitted: 20 
• Selection Criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY 
• OLDERADO: 1DDM Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-11-11 
• Released Date: 2000-04-10 
Deposition Author(s): Zwahlen, C., Li, S.C., Kay, L.E., Pawson, T., Forman-Kay, J.D.

Revision History  

• Version 1.0: 2000-04-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-16
  Changes: Data collection, Database references, Derived calculations, Experimental preparation