Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 13.82 kDa 
• Atom Count: 859 
• Residue Count: 106 
• Unique protein chains: 2

3TL0

Structure of SHP2 N-SH2 domain in complex with RLNpYAQLWHR peptide

• DOI: 10.2210/pdb3TL0/pdb

• Classification: HYDROLASE/Peptide
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-29 Released: 2011-09-28 
• Deposition Author(s): Zhang, Y., Zhang, J., Yuan, C., Hard, R.L., Park, I.H., Li, C., Bell, C.E., Pei, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.234 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Literature

Simultaneous binding of two peptidyl ligands by a SRC homology 2 domain.

Zhang, Y., Zhang, J., Yuan, C., Hard, R.L., Park, I.H., Li, C., Bell, C., Pei, D.

(2011) Biochemistry 50: 7637-7646

• PubMed: 21800896 
• DOI: 10.1021/bi200439v
• Primary Citation of Related Structures:  
  3TKZ, 3TL0


• PubMed Abstract: 
  

Src homology 2 (SH2) domains mediate protein-protein interactions by recognizing phosphotyrosine (pY)-containing sequences of target proteins. In all of the SH2 domain-pY peptide interactions described to date, the SH2 domain binds to a single pY peptide. Here, determination of the cocrystal structure of the N-terminal SH2 domain of phosphatase SHP-2 bound to a class IV peptide (VIpYFVP) revealed a noncanonical 1:2 (protein-peptide) complex. The first peptide binds in a canonical manner with its pY side chain inserted in the usual binding pocket, while the second pairs up with the first to form two antiparallel β-strands that extend the central β-sheet of the SH2 domain. This unprecedented binding mode was confirmed in the solution phase by NMR experiments and shown to be adopted by pY peptides derived from cellular proteins. Site-directed mutagenesis and surface plasmon resonance studies revealed that the binding of the first peptide is pY-dependent, but phosphorylation is not required for the second peptide. Our findings suggest a potential new function for the SH2 domain as a molecular clamp to promote dimerization of signaling proteins.

---

Organizational Affiliation: 

Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 11	A	109	Homo sapiens	Mutation(s): 0  Gene Names: PTPN11, PTP2C, SHPTP2 EC: 3.1.3.48
Find proteins for Q06124 (Homo sapiens) Explore Q06124  Go to UniProtKB:  Q06124
NIH Common Fund Data Resources
PHAROS:  Q06124 GTEx:  ENSG00000179295

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RLNpYAQLWHR peptide	B	10	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.234 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.749	α = 90
b = 62.749	β = 90
c = 75.323	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-08-29 
• Released Date: 2011-09-28 
Deposition Author(s): Zhang, Y., Zhang, J., Yuan, C., Hard, R.L., Park, I.H., Li, C., Bell, C.E., Pei, D.

Revision History 

• Version 1.0: 2011-09-28
  Type: Initial release