7OK7

Crystal structure of the UNC119B ARL3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

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This is version 1.3 of the entry. See complete history


Literature

The Structural and Biochemical Characterization of UNC119B Cargo Binding and Release Mechanisms.

Yelland, T.Garcia, E.Samarakoon, Y.Ismail, S.

(2021) Biochemistry 60: 1952-1963

  • DOI: https://doi.org/10.1021/acs.biochem.1c00251
  • Primary Citation of Related Structures:  
    7OK6, 7OK7

  • PubMed Abstract: 

    Two paralogs of the guanine dissociation inhibitor-like solubilizing factors UNC119, UNC119A and UNC119B, are present in the human genome. UNC119 binds to N-myristoylated proteins and masks the hydrophobic lipid from the hydrophilic cytosol, facilitating trafficking between different membranes. Two classes of UNC119 cargo proteins have been classified: low affinity cargoes, released by the Arf-like proteins ARL2 and ARL3, and high affinity cargoes, which are specifically released by ARL3 and trafficked to either the primary cilium or the immunological synapse. The UNC119 homologues have reported differences in functionality, but the structural and biochemical bases for these differences are unknown. Using myristoylated peptide binding and release assays, we show that peptides sharing the previously identified UNC119A high affinity motif show significant variations of binding affinities to UNC119B of up to 427-fold. Furthermore, we solve the first two crystal structures of UNC119B, one in complex with the high affinity cargo peptide of LCK and a second one in complex with the release factor ARL3. Using these novel structures, we identify a stretch of negatively charged amino acids unique to UNC119B that may undergo a conformational change following binding of a release factor which we propose as an additional release mechanism specific to UNC119B.


  • Organizational Affiliation

    Beatson Cancer Research UK Institute, Glasgow G61 1BD, Scotland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylation factor-like protein 3
A, B, C, D, E
A, B, C, D, E, F
183Mus musculusMutation(s): 0 
Gene Names: Arl3
UniProt
Find proteins for Q9WUL7 (Mus musculus)
Explore Q9WUL7 
Go to UniProtKB:  Q9WUL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WUL7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein unc-119 homolog B
G, H, I, J, K
G, H, I, J, K, L
183Homo sapiensMutation(s): 0 
Gene Names: UNC119B
UniProt & NIH Common Fund Data Resources
Find proteins for A6NIH7 (Homo sapiens)
Explore A6NIH7 
Go to UniProtKB:  A6NIH7
PHAROS:  A6NIH7
GTEx:  ENSG00000175970 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6NIH7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
M [auth A]
O [auth B]
Q [auth C]
T [auth D]
V [auth E]
M [auth A],
O [auth B],
Q [auth C],
T [auth D],
V [auth E],
X [auth F]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
BA [auth G]
FA [auth I]
HA [auth J]
IA [auth K]
JA [auth L]
BA [auth G],
FA [auth I],
HA [auth J],
IA [auth K],
JA [auth L],
R [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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CA [auth H],
EA [auth I],
GA [auth J],
Z [auth G]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth G],
DA [auth H]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
N [auth A]
P [auth B]
S [auth C]
U [auth D]
W [auth E]
N [auth A],
P [auth B],
S [auth C],
U [auth D],
W [auth E],
Y [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.27α = 90
b = 152.19β = 90
c = 171.84γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UK--

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2022-11-30
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description