7Q5U

The tandem SH2 domains of SYK with a bound CD3G diphospho-ITAM peptide

• PDB DOI: https://doi.org/10.2210/pdb7Q5U/pdb

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


• Deposited: 2021-11-04 Released: 2021-11-24 
• Deposition Author(s): Bradshaw, W.J., Katis, V.L., Chen, Z., Bountra, C., von Delft, F., Gileadi, O., Brennan, P.E.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.259 
• R-Value Work: 0.216 

Starting Model: experimental

Literature

The mechanism of allosteric activation of SYK kinase derived from multiple phospho-ITAM-bound structures

Bradshaw, W.J., Harris, G., Gileadi, O., Katis, V.L.

(2024) Structure 

• DOI: https://doi.org/10.1016/j.str.2024.09.024

Biological Assembly 1  

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

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

Biological Assembly Evidence: fluorescence resonance energy transfer

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 196.17 kDa 
• Atom Count: 14,063 
• Modelled Residue Count: 1,657 
• Deposited Residue Count: 1,710 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE], F [auth FFF]	265	Homo sapiens	Mutation(s): 0  Gene Names: SYK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens) Explore P43405  Go to UniProtKB:  P43405
PHAROS:  P43405 GTEx:  ENSG00000165025

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD3 gamma chain	G [auth GGG], H [auth HHH], I [auth III], J [auth JJJ], K [auth KKK], L [auth LLL]	20	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P09693 (Homo sapiens) Explore P09693  Go to UniProtKB:  P09693
PHAROS:  P09693 GTEx:  ENSG00000160654

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P4G	P [auth AAA], V [auth EEE]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C8 H18 O3 RRQYJINTUHWNHW-UHFFFAOYSA-N
PEG	O [auth AAA], Q [auth BBB], U [auth EEE], W [auth FFF]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	M [auth AAA], N [auth AAA], R [auth CCC], S [auth CCC], T [auth DDD]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	G [auth GGG], H [auth HHH], I [auth III], J [auth JJJ], K [auth KKK], L [auth LLL]	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.259 
• R-Value Work: 0.216 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.321	α = 90
b = 129.312	β = 100.232
c = 95.346	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Bradshaw, W.J., Katis, V.L., Chen, Z., Bountra, C., von Delft, F., Gileadi, O., Brennan, P.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	5U54AG065187-03

Revision History  

• Version 1.0: 2021-11-24
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary
• Version 1.3: 2024-10-30
  Changes: Database references