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: 18.79 kDa 
• Atom Count: 1220 
• Modelled Residue Count: 154 
• Deposited Residue Count: 167 
• Unique protein chains: 2

2NMB

DNUMB PTB DOMAIN COMPLEXED WITH A PHOSPHOTYROSINE PEPTIDE, NMR, ENSEMBLE OF STRUCTURES.

• PDB DOI: 10.2210/pdb2NMB/pdb
• BMRB: 4263

• Classification: CELL CYCLE/GENE REGULATION
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-10-29 Released: 1998-11-04 
• Deposition Author(s): Li, S.-C., Zwahlen, C., Vincent, S.J.F., McGlade, C.J., Pawson, T., Forman-Kay, J.D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 14 
• Selection Criteria: NO NOE VIOLATION > 0.3 A 

Literature

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: 1075-1083

• PubMed: 9846878 
• DOI: 10.1038/4185
• Primary Citation of Related Structures:  
  2NMB


• PubMed Abstract: 
  

The phosphotyrosine-binding (PTB) domain of Numb, a protein involved in asymmetric cell division, has recently been shown to bind to the adapter protein Lnx through an LDNPAY sequence, to the Numb-associated kinase (Nak) through a sequence that does not contain an NPXY motif and to GP(p)Y-containing peptides obtained from library screening. We show here that these diverse peptide sequences bind with comparable affinities to the Numb PTB domain at a common binding site on the surface of the protein. The NMR structure of the Numb PTB domain in complex with a GPpY-containing peptide reveals a novel mechanism of binding with the peptide in a helical turn that does not hydrogen bond to the PTB domain beta-sheet. These results suggest that PTB domains can potentially have multiple modes of peptide recognition and provide a structural basis from which the multiple functions of the Numb PTB domain during asymmetric cell division could arise.

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Related Citations: 

• High-Affinity Binding of the Drosophila Numb Phosphotyrosine-Binding Domain to Pep Tides Containing a Gly-Pro-(P)Tyr Motif
  Li, S.-C., Songyang, Z., Vincent, S.J.F., Zwahlen, C., Wiley, S., Cantley, L., Kay, L.E., Forman-Kay, J.D., Pawson, T.
  (1997) Proc Natl Acad Sci U S A 94: 7204

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Organizational Affiliation: 

Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Department of Molecular and Medical Genetics, University of Toronto, Ontario, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (NUMB PROTEIN)	A	160	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
PROTEIN (GPPY PEPTIDE)	B	7	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 14 
• Selection Criteria: NO NOE VIOLATION > 0.3 A 
• OLDERADO: 2NMB Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-10-29 
• Released Date: 1998-11-04 
Deposition Author(s): Li, S.-C., Zwahlen, C., Vincent, S.J.F., McGlade, C.J., Pawson, T., Forman-Kay, J.D.

Revision History  

• Version 1.0: 1998-11-04
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-16
  Changes: Database references, Derived calculations