6H6A | pdb_00006h6a

Crystal structure of UNC119 in complex with LCK peptide

PDB DOI: https://doi.org/10.2210/pdb6H6A/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-07-26 Released: 2018-09-26
Deposition Author(s): Yelland, T., ElMaghloob, Y., McIlwraith, M., Stephen, L., Ismail, S.
Funding Organization(s): Cancer Research UK

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.212 (Depositor), 0.216 (DCC)
R-Value Work:
0.171 (Depositor), 0.181 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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

PubMed: 30220567 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.devcel.2018.08.012
Primary Citation 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. 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.

Macromolecule Content

Total Structure Weight: 70.25 kDa
Atom Count: 4,672
Modeled Residue Count: 513
Deposited Residue Count: 576
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein unc-119 homolog A	A [auth D]	182	Homo sapiens	Mutation(s): 0 Gene Names: UNC119, RG4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13432 (Homo sapiens) Explore Q13432 Go to UniProtKB: Q13432
PHAROS: Q13432 GTEx: ENSG00000109103
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13432
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-CYS-GLY-CYS-SER-SER	B [auth E], D [auth H], F [auth K]	10	Homo sapiens	Mutation(s): 0 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 GTEx: ENSG00000182866
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06239
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein unc-119 homolog A	C [auth G], E [auth J]	182	Homo sapiens	Mutation(s): 0 Gene Names: UNC119, RG4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13432 (Homo sapiens) Explore Q13432 Go to UniProtKB: Q13432
PHAROS: Q13432 GTEx: ENSG00000109103
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13432
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
15P Query on 15P Download:Ideal Coordinates CCD File SDF format, chain I [auth D] MOL2 format, chain I [auth D] mmCIF format, chain I [auth D]	I [auth D]	POLYETHYLENE GLYCOL (N=34) C₆₉ H₁₄₀ O₃₅ VUYXVWGKCKTUMF-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Interactions & Density Focus chain I [auth D]
MYR Query on MYR Download:Ideal Coordinates CCD File SDF format, chain S [auth K] SDF format, chain N [auth H] SDF format, chain J [auth E] MOL2 format, chain S [auth K] MOL2 format, chain N [auth H] MOL2 format, chain J [auth E] mmCIF format, chain S [auth K] mmCIF format, chain N [auth H] mmCIF format, chain J [auth E]	J [auth E], N [auth H], S [auth K]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain J [auth E] Focus chain N [auth H] Focus chain S [auth K] Interactions & Density Focus chain J [auth E] Focus chain N [auth H] Focus chain S [auth K]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain R [auth J] SDF format, chain M [auth G] MOL2 format, chain R [auth J] MOL2 format, chain M [auth G] mmCIF format, chain R [auth J] mmCIF format, chain M [auth G]	M [auth G], R [auth J]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth G] Focus chain R [auth J] Interactions & Density Focus chain M [auth G] Focus chain R [auth J]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Q [auth J] SDF format, chain P [auth J] SDF format, chain O [auth J] SDF format, chain L [auth G] SDF format, chain K [auth G] SDF format, chain H [auth D] SDF format, chain G [auth D] MOL2 format, chain Q [auth J] MOL2 format, chain P [auth J] MOL2 format, chain O [auth J] MOL2 format, chain L [auth G] MOL2 format, chain K [auth G] MOL2 format, chain H [auth D] MOL2 format, chain G [auth D] mmCIF format, chain Q [auth J] mmCIF format, chain P [auth J] mmCIF format, chain O [auth J] mmCIF format, chain L [auth G] mmCIF format, chain K [auth G] mmCIF format, chain H [auth D] mmCIF format, chain G [auth D]	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		Interactions Focus chain G [auth D] Focus chain H [auth D] Focus chain K [auth G] Focus chain L [auth G] Focus chain O [auth J] Focus chain P [auth J] Focus chain Q [auth J] Interactions & Density Focus chain G [auth D] Focus chain H [auth D] Focus chain K [auth G] Focus chain L [auth G] Focus chain O [auth J] Focus chain P [auth J] Focus chain Q [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.212 (Depositor), 0.216 (DCC)
R-Value Work: 0.171 (Depositor), 0.181 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.09	α = 90
b = 63.62	β = 90
c = 188.16	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-09-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Cancer Research UK	United 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
Version 1.4: 2024-10-23
Changes: Data collection, Database references, Refinement description, Structure summary