5KAZ | pdb_00005kaz

Human SH2D1B structure

• PDB DOI: https://doi.org/10.2210/pdb5KAZ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2016-06-02 Released: 2017-04-12 
• Deposition Author(s): Taha, M., Nezerwa, E., Nam, H.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

The X-ray Crystallographic Structure of Human EAT2 (SH2D1B).

Taha, M., Nezerwa, E., Nam, H.J.

(2016) Protein Pept Lett 23: 862-866

• PubMed: 27586300 
• DOI: https://doi.org/10.2174/0929866523666160831162239
• Primary Citation Related Structures: 
  5KAZ


• PubMed Abstract: 
  

  Ewing's Sarcoma transcript-2 (EAT2) also known as SH2D1B is involved in regulation of signalling lymphocytic activation molecule (SLAM) family receptor functions. Cytoplasmic tails of SLAM family receptors contain tyrosine residues which mediate the downstream signal transduction through their phosphorylation. EAT2, composed of a single SH2 domain and a short C-terminal tail, binds to the phosphotyrosine residues and regulates SLAM family receptor signalling. We have determined the crystal structure of the human EAT2 protein in an unliganded form. Compared with the mouse EAT2-peptide complex structure, we observe conformational differences in the loops involved in ligand binding. When compared with SAP, the other single SH2 domain protein in human, EAT2 shows similar binding energies to unphosphorylated ligands. This is inconsistent to the previous data showing low affinity of EAT2 toward unphosphorylated peptides compared to SAP which shows high affinity. Additional factors other than the SH2 domains may contribute to the reported differences.

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Organizational Affiliation: 
• Department of Bioengineering, The University of Texas at Dallas, 800 W. Campbell Rd, RL10, Richardson, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.19 kDa 
• Atom Count: 999 
• Modeled Residue Count: 103 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SH2 domain-containing protein 1B	A	104	Homo sapiens	Mutation(s): 0  Gene Names: SH2D1B, EAT2
UniProt & NIH Common Fund Data Resources
Find proteins for O14796 (Homo sapiens) Explore O14796  Go to UniProtKB:  O14796
PHAROS:  O14796 GTEx:  ENSG00000198574

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.983	α = 90
b = 66.983	β = 90
c = 105.155	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-12 
Deposition Author(s): Taha, M., Nezerwa, E., Nam, H.-J.

Revision History  

• Version 1.0: 2017-04-12
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references