1RRG | pdb_00001rrg

NON-MYRISTOYLATED RAT ADP-RIBOSYLATION FACTOR-1 COMPLEXED WITH GDP, DIMERIC CRYSTAL FORM

• PDB DOI: https://doi.org/10.2210/pdb1RRG/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1995-12-16 Released: 1996-06-20 
• Deposition Author(s): Greasley, S.E., Jhoti, H., Bax, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.315 (Depositor) 
• R-Value Work: 
  0.187 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

The structure of rat ADP-ribosylation factor-1 (ARF-1) complexed to GDP determined from two different crystal forms.

Greasley, S.E., Jhoti, H., Teahan, C., Solari, R., Fensome, A., Thomas, G.M., Cockcroft, S., Bax, B.

(1995) Nat Struct Biol 2: 797-806

• PubMed: 7552752 
• DOI: https://doi.org/10.1038/nsb0995-797
• Primary Citation Related Structures: 
  1RRF, 1RRG


• PubMed Abstract: 
  

  The ARFs are a family of 21,000 M(r) proteins with biological roles in constitutive secretion and activation of phospholipase D. The structure of ARF-1 complexed to GDP determined from two crystal forms reveals a topology that is similar to that of the protein p21 ras with two differences: an additional amino-terminal helix and an extra beta-strand. The Mg2+ ion in ARF-1 displays a five-coordination sphere; this feature is not seen in p21 ras, due to a shift in the relative position of the DXXG motif between the two proteins. The occurrence of a dimer in one crystal form suggests that ARF-1 may dimerize during its biological function. The dimer interface involves a region of the ARF-1 molecule that is analogous to the effector domain in p21 ras and may mediate interactions with its effectors.

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Organizational Affiliation: 
• Glaxo Research & Development, Department of Biomolecular Structure, Stevenage, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 42.38 kDa 
• Atom Count: 3,104 
• Modeled Residue Count: 354 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAT ADP-RIBOSYLATION FACTOR-1	A, B	181	Rattus norvegicus	Mutation(s): 0  EC: 3.6.5.2
UniProt
Find proteins for P84079 (Rattus norvegicus) Explore P84079  Go to UniProtKB:  P84079

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	D [auth A], F [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.315 (Depositor) 
• R-Value Work:  0.187 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.36	α = 90
b = 45.01	β = 133.62
c = 91.96	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-06-20 
Deposition Author(s): Greasley, S.E., Jhoti, H., Bax, B.

Revision History  

• Version 1.0: 1996-06-20
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other