Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 20.52 kDa 
• Atom Count: 1522 
• Modelled Residue Count: 173 
• Deposited Residue Count: 174 
• Unique protein chains: 1

1E0S

small G protein Arf6-GDP

• PDB DOI: 10.2210/pdb1E0S/pdb

• Classification: G PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-04-06 Released: 2000-04-18 
• Deposition Author(s): Menetrey, J., Cherfils, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.234 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 

Literature

Structure of Arf6-Gdp Suggests a Basis for Guanine Nucleotide Exchange Factors Specificity

Menetrey, J., Macia, E., Pasqualato, S., Franco, M., Cherfils, J.

(2000) Nat Struct Biol 7: 466

• PubMed: 10881192 
• DOI: 10.1038/75863
• Primary Citation of Related Structures:  
  1E0S


• PubMed Abstract: 
  

Arf6 is an isoform of Arf that localizes at the periphery of the cell where it has an essential role in endocytotic pathways. Its function does not overlap with that of Arf1, although the two proteins share approximately 70% sequence identity and they have switch regions, whose conformation depends on the nature of the guanine nucleotide, with almost identical sequences. The crystal structure of Arf6-GDP at 2.3 A shows that it has a conformation similar to that of Arf1-GDP, which cannot bind membranes with high affinity. Significantly, the switch regions of Arf6 deviate by 2-5 A from those of Arf1. These differences are a consequence of the shorter N-terminal linker of Arf6 and of discrete sequence changes between Arf6 and Arf1. Mutational analysis shows that one of the positions which differs between Arf1 and Arf6 affects the configuration of the nucleotide binding site and thus the nucleotide binding properties of the Arf variant. Altogether, our results provide a structural basis for understanding how Arf1 and Arf6 can be distinguished by their guanine nucleotide exchange factors and suggest a model for the nucleotide/membrane cycle of Arf6.

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Organizational Affiliation: 

Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif-sur-Yvette, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor 6	A	174	Homo sapiens	Mutation(s): 0  Gene Names: ARF6
UniProt & NIH Common Fund Data Resources
Find proteins for P62330 (Homo sapiens) Explore P62330  Go to UniProtKB:  P62330
PHAROS:  P62330 GTEx:  ENSG00000165527

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
BME	C [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
NH4	D [auth A]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.234 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.66	α = 90
b = 55.66	β = 90
c = 194.95	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-04-06 
• Released Date: 2000-04-18 
Deposition Author(s): Menetrey, J., Cherfils, J.

Revision History  

• Version 1.0: 2000-04-18
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-09-25
  Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary