8EZJ

Cryo-EM structure of the S. cerevisiae Arf-like protein Arl1 bound to the Arf guanine nucleotide exchange factor Gea2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insight into an Arl1-ArfGEF complex involved in Golgi recruitment of a GRIP-domain golgin.

Duan, H.D.Jain, B.K.Li, H.Graham, T.R.Li, H.

(2024) Nat Commun 15: 1942-1942

  • DOI: https://doi.org/10.1038/s41467-024-46304-w
  • Primary Citation of Related Structures:  
    8EZJ, 8EZQ

  • PubMed Abstract: 

    Arl1 is an Arf-like (Arl) GTP-binding protein that interacts with the guanine nucleotide exchange factor Gea2 to recruit the golgin Imh1 to the Golgi. The Arl1-Gea2 complex also binds and activates the phosphatidylserine flippase Drs2 and these functions may be related, although the underlying molecular mechanism is unclear. Here we report high-resolution cryo-EM structures of the full-length Gea2 and the Arl1-Gea2 complex. Gea2 is a large protein with 1459 residues and is composed of six domains (DCB, HUS, SEC7, HDS1-3). We show that Gea2 assembles a stable dimer via an extensive interface involving hydrophobic and electrostatic interactions in the DCB and HUS region. Contrary to the previous report on a Gea2 homolog in which Arl1 binds to the dimerization surface of the DCB domain, implying a disrupted dimer upon Arl1 binding, we find that Arl1 binds to the outside surface of the Gea2 DCB domain, leaving the Gea2 dimer intact. The interaction between Arl1 and Gea2 involves the classic FWY aromatic residue triad as well as two Arl1-specific residues. We show that key mutations that disrupt the Arl1-Gea2 interaction abrogate Imh1 Golgi association. This work clarifies the Arl1-Gea2 interaction and improves our understanding of molecular events in the membrane trafficking.


  • Organizational Affiliation

    Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ARF guanine-nucleotide exchange factor 2
A, B
1,483Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GEA2YEL022W
UniProt
Find proteins for P39993 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39993 
Go to UniProtKB:  P39993
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39993
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylation factor-like protein 1
C, D
183Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: ARL1ARF3YBR164CYBR1216
UniProt
Find proteins for P38116 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38116 
Go to UniProtKB:  P38116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38116
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA231466

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references, Structure summary