8JCA

Cyrstal structure of SKIP RUN domain in complex with GTP-bound Arl8b(Q75L)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

Starting Models: experimental, in silico
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Mechanistic Insights into the Interactions of Arl8b with the RUN Domains of PLEKHM1 and SKIP.

Qiu, X.Li, Y.Wang, Y.Gong, X.Wang, Y.Pan, L.

(2023) J Mol Biol 435: 168293-168293

  • DOI: https://doi.org/10.1016/j.jmb.2023.168293
  • Primary Citation of Related Structures:  
    8JC5, 8JCA

  • PubMed Abstract: 

    Arl8b, a specific Arf-like family GTPase present on lysosome, and plays critical roles in many lysosome-related cellular processes such as autophagy. The active Arl8b can be specifically recognized by the RUN domains of two Arl8b-effectors PLEKHM1 and SKIP, thereby regulating the autophagosome/lysosome membrane fusion and the intracellular lysosome positioning, respectively. However, the mechanistic bases underlying the interactions of Arl8b with the RUN domains of PLEKHM1 and SKIP remain elusive. Here, we report the two high-resolution crystal structures of the active Arl8b in complex with the RUN domains of PLEKHM1 and SKIP. In addition to elucidating the detailed molecular mechanism governing the specific interactions of the active Arl8b with the RUN domains of PLEKHM1 and SKIP, the determined complex structures also reveal a general binding mode shared by the PLEKHM1 and SKIP RUN domains for interacting with the active Arl8b. Furthermore, we uncovered a competitive relationship between the RUN domains of PLEKHM1 and SKIP in binding to the active Arl8b as well as a unique small GTPase-binding mode adopted by the PLEKHM1 and SKIP RUN domains, thereby enriching the repertoire of the RUN domain/small GTPase interaction modes. In all, our findings provide new mechanistic insights into the interactions of the active Arl8b with PLEKHM1 and SKIP, and are valuable for further understanding the working modes of these proteins in relevant cellular processes.


  • Organizational Affiliation

    College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, Sichuan 610068, China; State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylation factor-like protein 8B169Homo sapiensMutation(s): 1 
Gene Names: ARL8BARL10CGIE1
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVJ2 (Homo sapiens)
Explore Q9NVJ2 
Go to UniProtKB:  Q9NVJ2
PHAROS:  Q9NVJ2
GTEx:  ENSG00000134108 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NVJ2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pleckstrin homology domain-containing family M member 2165Homo sapiensMutation(s): 0 
Gene Names: PLEKHM2KIAA0842SKIP
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IWE5 (Homo sapiens)
Explore Q8IWE5 
Go to UniProtKB:  Q8IWE5
PHAROS:  Q8IWE5
GTEx:  ENSG00000116786 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IWE5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.687α = 90
b = 53.836β = 98.13
c = 40.512γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21822705

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release