1MR3

Saccharomyces cerevisiae ADP-ribosylation Factor 2 (ScArf2) complexed with GDP-3'P at 1.6A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structures of yeast ARF2 and ARL1: distinct roles for the N terminus in the structure and function of ARF family GTPases.

Amor, J.C., Horton, J.R., Zhu, X., Wang, Y., Sullards, C., Ringe, D., Cheng, X., Kahn, R.A.

(2001) J Biol Chem 276: 42477-42484

  • DOI: 10.1074/jbc.M106660200
  • Primary Citation of Related Structures:  
    1MOZ, 1MR3

  • PubMed Abstract: 

    • Structures were determined by x-ray crystallography for two members of the ADP-ribosylation factor (ARF) family of regulatory GTPases, yeast ARF1 and ARL1, and were compared with previously determined structures of human ARF1 and ARF6. These analyses revealed an overall conserved fold but differences in primary sequence and length, particularly in an N-terminal loop, lead to differences in nucleotide and divalent metal binding ...

    Structures were determined by x-ray crystallography for two members of the ADP-ribosylation factor (ARF) family of regulatory GTPases, yeast ARF1 and ARL1, and were compared with previously determined structures of human ARF1 and ARF6. These analyses revealed an overall conserved fold but differences in primary sequence and length, particularly in an N-terminal loop, lead to differences in nucleotide and divalent metal binding. Packing of hydrophobic residues is central to the interplay between the N-terminal alpha-helix, switch I, and the interswitch region, which along with differences in surface electrostatics provide explanations for the different biophysical and biochemical properties of ARF and ARF-like proteins.

    Organizational Affiliation: 

    Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322-3050, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-ribosylation factor 2A [auth F]181Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ARF2
UniProt
Find proteins for P19146 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P19146 
Go to UniProtKB:  P19146
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19146
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G3D
Query on G3D
Download Ideal Coordinates CCD File 
C [auth F]GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE
C10 H16 N5 O14 P3
HEYSFDAMRDTCJM-UUOKFMHZSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
N [auth F],
O [auth F]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
PDO
Query on PDO
Download Ideal Coordinates CCD File 
T [auth F],
U [auth F]		1,3-PROPANDIOL
C3 H8 O2
YPFDHNVEDLHUCE-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
D [auth F],
E [auth F],
F,
G [auth F],
H [auth F],
D [auth F],
E [auth F],
F,
G [auth F],
H [auth F],
I [auth F],
J [auth F],
K [auth F],
L [auth F],
M [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
EOH
Query on EOH
Download Ideal Coordinates CCD File 
P [auth F],
Q [auth F],
R [auth F],
S [auth F]		ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
B [auth F]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.822α = 90
b = 69.47β = 90
c = 40.861γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-20
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description