1MOZ | pdb_00001moz

ADP-ribosylation factor-like 1 (ARL1) from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb1MOZ/pdb

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


• Deposited: 2002-09-10 Released: 2002-10-09 
• Deposition Author(s): Amor, J.C., Horton, J.R., Zhu, X., Wang, Y., Sullards, C., Ringe, D., Cheng, X., Kahn, R.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free: 
  0.246 (Depositor) 
• R-Value Work: 
  0.206 (Depositor) 
• R-Value Observed: 
  0.240 (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.

---

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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.8 kDa 
• Atom Count: 2,732 
• Modeled Residue Count: 356 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor-like protein 1	A, B	183	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38116 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38116  Go to UniProtKB:  P38116

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A], D [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free:  0.246 (Depositor) 
• R-Value Work:  0.206 (Depositor) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.25	α = 90
b = 104.25	β = 90
c = 45.69	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
GLRF	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-09 
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: 2002-10-09
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary