Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 13.09 kDa 
• Atom Count: 1102 
• Residue Count: 108 
• Unique protein chains: 2

2CIA

human nck2 sh2-domain in complex with a decaphosphopeptide from translocated intimin receptor (tir) of epec

• DOI: 10.2210/pdb2CIA/pdb

• Classification: SH2-DOMAIN
• Organism(s): Homo sapiens, Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-03-17 Released: 2006-04-24 
• Deposition Author(s): Frese, S., Schubert, W.-D., Findeis, A.C., Marquardt, T., Roske, Y.S., Stradal, T.E.B., Heinz, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.170 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 

Literature

The Phosphotyrosine Peptide Binding Specificity of Nck1 and Nck2 Src Homology 2 Domains.

Frese, S., Schubert, W.-D., Findeis, A.C., Marquardt, T., Roske, Y.S., Stradal, T.E.B., Heinz, D.W.

(2006) J Biol Chem 281: 18236

• PubMed: 16636066 
• DOI: 10.1074/jbc.M512917200
• Primary Citation of Related Structures:  
  2CI9, 2CI8, 2CIA


• PubMed Abstract: 
  

Nck proteins are essential Src homology (SH) 2 and SH3 domain-bearing adapters that modulate actin cytoskeleton dynamics by linking proline-rich effector molecules to tyrosine kinases or phosphorylated signaling intermediates. Two mammalian pathogens, enteropathogenic Escherichia coli and vaccinia virus, exploit Nck as part of their infection strategy. Conflicting data indicate potential differences in the recognition specificities of the SH2 domains of the isoproteins Nck1 (Nckalpha) and Nck2 (Nckbeta and Grb4). We have characterized the binding specificities of both SH2 domains and find them to be essentially indistinguishable. Crystal structures of both domains in complex with phosphopeptides derived from the enteropathogenic E. coli protein Tir concur in identifying highly conserved, specific recognition of the phosphopeptide. Differential peptide recognition can therefore not account for the preference of either Nck in particular signaling pathways. Binding studies using sequentially mutated, high affinity phosphopeptides establish the sequence variability tolerated in peptide recognition. Based on this binding motif, we identify potential new binding partners of Nck1 and Nck2 and confirm this experimentally for the Arf-GAP GIT1.

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Organizational Affiliation: 

Division of Cell Biology, German Research Center for Biotechnology, Mascheroder Weg 1, D-38124 Braunschweig, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOPLASMIC PROTEIN NCK2	A	102	Homo sapiens	Mutation(s): 0  Gene Names: NCK2, GRB4
Find proteins for O43639 (Homo sapiens) Explore O43639  Go to UniProtKB:  O43639
NIH Common Fund Data Resources
PHAROS  O43639 GTEx  ENSG00000071051

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSLOCATED INTIMIN RECEPTOR	L	11	Escherichia coli	Mutation(s): 0
Find proteins for B7UM99 (Escherichia coli O127:H6 (strain E2348/69 / EPEC)) Explore B7UM99  Go to UniProtKB:  B7UM99

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	A	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
IPA	A	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.170 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.244	α = 90
b = 52.188	β = 90
c = 58.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-03-17 
• Released Date: 2006-04-24 
Deposition Author(s): Frese, S., Schubert, W.-D., Findeis, A.C., Marquardt, T., Roske, Y.S., Stradal, T.E.B., Heinz, D.W.

Revision History 

• Version 1.0: 2006-04-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2019-05-29
  Changes: Data collection, Derived calculations, Experimental preparation, Other