1MR3 | pdb_00001mr3

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

• PDB DOI: https://doi.org/10.2210/pdb1MR3/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-09-17 Released: 2002-11-20 
• Deposition Author(s): Amor, J.-C., Horton, J.R., Zhu, X., Wang, Y., Sullards, C., Ringe, D., Cheng, X., Kahn, R.A.

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Experimental Data Snapshot

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

Starting Model: experimental

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 Biological Chem 276: 42477-42484

• PubMed: 11535602 
• DOI: https://doi.org/10.1074/jbc.M106660200
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322-3050, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.37 kDa 
• Atom Count: 1,830 
• Modeled Residue Count: 177 
• Deposited Residue Count: 181 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor 2	A [auth F]	181	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: ARF2
UniProt
Find proteins for P19146 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P19146  Go to UniProtKB:  P19146

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G3D	C [auth F]	GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE C10 H16 N5 O14 P3 HEYSFDAMRDTCJM-UUOKFMHZSA-N
GOL	N [auth F], O [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PDO	T [auth F], U [auth F]	1,3-PROPANDIOL C3 H8 O2 YPFDHNVEDLHUCE-UHFFFAOYSA-N
EDO	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
EOH	P [auth F], Q [auth F], R [auth F], S [auth F]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
MG	B [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.822	α = 90
b = 69.47	β = 90
c = 40.861	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-20 
Deposition Author(s): Amor, J.-C., Horton, J.R., Zhu, X., Wang, Y., Sullards, C., Ringe, D., Cheng, X., Kahn, R.A.

Revision History  

• 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
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description