5EE5

Structure of human ARL1 in complex with the DCB domain of BIG1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.279 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Insights into Arl1-Mediated Targeting of the Arf-GEF BIG1 to the trans-Golgi.

Galindo, A.Soler, N.McLaughlin, S.H.Yu, M.Williams, R.L.Munro, S.

(2016) Cell Rep 16: 839-850

  • DOI: 10.1016/j.celrep.2016.06.022

  • PubMed Abstract: 
  • The GTPase Arf1 is the major regulator of vesicle traffic at both the cis- and trans-Golgi. Arf1 is activated at the cis-Golgi by the guanine nucleotide exchange factor (GEF) GBF1 and at the trans-Golgi by the related GEF BIG1 or its paralog, BIG2. T ...

    The GTPase Arf1 is the major regulator of vesicle traffic at both the cis- and trans-Golgi. Arf1 is activated at the cis-Golgi by the guanine nucleotide exchange factor (GEF) GBF1 and at the trans-Golgi by the related GEF BIG1 or its paralog, BIG2. The trans-Golgi-specific targeting of BIG1 and BIG2 depends on the Arf-like GTPase Arl1. We find that Arl1 binds to the dimerization and cyclophilin binding (DCB) domain in BIG1 and report a crystal structure of human Arl1 bound to this domain. Residues in the DCB domain that bind Arl1 are required for BIG1 to locate to the Golgi in vivo. DCB domain-binding residues in Arl1 have a distinct conformation from those in known Arl1-effector complexes, and this plasticity allows Arl1 to interact with different effectors of unrelated structure. The findings provide structural insight into how Arf1 GEFs, and hence active Arf1, achieve their correct subcellular distribution.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Brefeldin A-inhibited guanine nucleotide-exchange protein 1
A
213Homo sapiensMutation(s): 0 
Gene Names: ARFGEF1 (ARFGEP1, BIG1)
Find proteins for Q9Y6D6 (Homo sapiens)
Go to Gene View: ARFGEF1
Go to UniProtKB:  Q9Y6D6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ADP-ribosylation factor-like protein 1
B
171Homo sapiensMutation(s): 0 
Gene Names: ARL1
Find proteins for P40616 (Homo sapiens)
Go to Gene View: ARL1
Go to UniProtKB:  P40616
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GTP
Query on GTP

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B
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
A
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.279 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.166α = 90.00
b = 50.727β = 111.98
c = 103.837γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata reduction
PHASERphasing
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-13
    Type: Database references
  • Version 1.2: 2016-07-27
    Type: Database references