6H6A

Crystal structure of UNC119 in complex with LCK peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The Ciliary Machinery Is Repurposed for T Cell Immune Synapse Trafficking of LCK.

Stephen, L.A.ElMaghloob, Y.McIlwraith, M.J.Yelland, T.Castro Sanchez, P.Roda-Navarro, P.Ismail, S.

(2018) Dev Cell 47: 122-132.e4

  • DOI: 10.1016/j.devcel.2018.08.012
  • Primary Citation of Related Structures:  
    6H6A

  • PubMed Abstract: 
  • Upon engagement of the T cell receptor with an antigen-presenting cell, LCK initiates TCR signaling by phosphorylating its activation motifs. However, the mechanism of LCK activation specifically at the immune synapse is a major question. We show that phosphorylation of the LCK activating Y394, despite modestly increasing its catalytic rate, dramatically focuses LCK localization to the immune synapse ...

    Upon engagement of the T cell receptor with an antigen-presenting cell, LCK initiates TCR signaling by phosphorylating its activation motifs. However, the mechanism of LCK activation specifically at the immune synapse is a major question. We show that phosphorylation of the LCK activating Y394, despite modestly increasing its catalytic rate, dramatically focuses LCK localization to the immune synapse. We describe a trafficking mechanism whereby UNC119A extracts membrane-bound LCK by sequestering the hydrophobic myristoyl group, followed by release at the target membrane under the control of the ciliary ARL3/ARL13B. The UNC119A N terminus acts as a "regulatory arm" by binding the LCK kinase domain, an interaction inhibited by LCK Y394 phosphorylation, thus together with the ARL3/ARL13B machinery ensuring immune synapse focusing of active LCK. We propose that the ciliary machinery has been repurposed by T cells to generate and maintain polarized segregation of signals such as activated LCK at the immune synapse.


    Organizational Affiliation

    CR-UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow G12 8QQ, UK. Electronic address: s.ismail@beatson.gla.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein unc-119 homolog AA [auth D]182Homo sapiensMutation(s): 0 
Gene Names: UNC119RG4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13432 (Homo sapiens)
Explore Q13432 
Go to UniProtKB:  Q13432
PHAROS:  Q13432
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13432
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GLY-CYS-GLY-CYS-SER-SERB [auth E],
D [auth H],
F [auth K]
10Homo sapiensMutation(s): 0 
Gene Names: LCK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P06239 (Homo sapiens)
Explore P06239 
Go to UniProtKB:  P06239
PHAROS:  P06239
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UniProt GroupP06239
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein unc-119 homolog AC [auth G],
E [auth J]
182Homo sapiensMutation(s): 0 
Gene Names: UNC119RG4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13432 (Homo sapiens)
Explore Q13432 
Go to UniProtKB:  Q13432
PHAROS:  Q13432
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13432
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
15P
Query on 15P

Download Ideal Coordinates CCD File 
I [auth D]POLYETHYLENE GLYCOL (N=34)
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
 Ligand Interaction
MYR
Query on MYR

Download Ideal Coordinates CCD File 
J [auth E],
N [auth H],
S [auth K]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
M [auth G],
R [auth J]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth D],
H [auth D],
K [auth G],
L [auth G],
O [auth J],
G [auth D],
H [auth D],
K [auth G],
L [auth G],
O [auth J],
P [auth J],
Q [auth J]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.09α = 90
b = 63.62β = 90
c = 188.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2019-11-27
    Changes: Derived calculations