Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.89 kDa 
• Atom Count: 990 
• Modelled Residue Count: 105 
• Deposited Residue Count: 110 
• Unique protein chains: 2

3MXC

Structures of Grb2-SH2 Domain and AICD peptide Complexes Reveal a Conformational Switch and Their Functional Implications.

• DOI: 10.2210/pdb3MXC/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-07 Released: 2011-05-11 
• Deposition Author(s): Sen, U., Das, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.244 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

Literature

Functional Implications of the Conformational Switch in AICD Peptide upon Binding to Grb2-SH2 Domain.

Das, S., Raychaudhuri, M., Sen, U., Mukhopadhyay, D.

(2011) J Mol Biol 414: 217-230

• PubMed: 22001015 
• DOI: 10.1016/j.jmb.2011.09.046
• Primary Citation of Related Structures:  
  3MXC, 3MXY


• PubMed Abstract: 
  

It has been hypothesized previously that synergistic effect of both amyloid precursor protein intracellular C-terminal domain (AICD) and Aβ aggregation could contribute to Alzheimer's disease pathogenesis. Structural studies of AICD have found no stable globular fold over a broad range of pH. Present work is based on the premises that a conformational switch involving the flipping of C-terminal helix of AICD would be essential for effective binding with the Src homology 2 (SH2) domain of growth factor receptor binding protein-2 (Grb2) and subsequent initiation of Grb2-mediated endo-lysosomal pathway. High-resolution crystal structures of Grb2-SH2 domain bound to AICD peptides reveal a unique mode of binding where the peptides assume a noncanonical conformation that is unlike other structures of AICD peptides bound to protein-tyrosine-binding domains or that of its free state; rather, a flipping of the C-terminal helix of AICD is evident. The involvement of different AICD residues in Grb2-SH2 interaction is further elucidated through fluorescence-based assays. Our results reveal the significance of a specific interaction of the two molecules to optimize the rapid transport of AICD inside endosomal vesicles presumably to reduce the cytotoxic load.

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Organizational Affiliation: 

Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, WB, Kolkata 700 064, India.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Growth factor receptor-bound protein 2	A	101	Homo sapiens	Mutation(s): 0  Gene Names: GRB2, ASH
Find proteins for P62993 (Homo sapiens) Explore P62993  Go to UniProtKB:  P62993
NIH Common Fund Data Resources
PHAROS:  P62993 GTEx:  ENSG00000177885

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AICD peptide	B [auth L]	9	N/A	Mutation(s): 0
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
NIH Common Fund Data Resources
PHAROS:  P05067

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.244 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.369	α = 90
b = 59.369	β = 90
c = 117.101	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
CNS	refinement
AUTOMAR	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-05-07 
• Released Date: 2011-05-11 
Deposition Author(s): Sen, U., Das, S.

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-10-12
  Changes: Database references
• Version 1.3: 2011-11-02
  Changes: Database references
• Version 1.4: 2011-12-14
  Changes: Database references