Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 73.17 kDa 
• Atom Count: 4561 
• Modelled Residue Count: 550 
• Deposited Residue Count: 640 
• Unique protein chains: 2

1I4D

CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP COMPLEXED WITH ARFAPTIN (P21)

• PDB DOI: 10.2210/pdb1I4D/pdb
• BMRB: 5511

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


• Deposited: 2001-02-20 Released: 2001-05-16 
• Deposition Author(s): Tarricone, C., Xiao, B., Justin, N., Gamblin, S.J., Smerdon, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.298 
• R-Value Work: 0.238 

Literature

The structural basis of Arfaptin-mediated cross-talk between Rac and Arf signalling pathways.

Tarricone, C., Xiao, B., Justin, N., Walker, P.A., Rittinger, K., Gamblin, S.J., Smerdon, S.J.

(2001) Nature 411: 215-219

• PubMed: 11346801 
• DOI: 10.1038/35075620
• Primary Citation of Related Structures:  
  1I49, 1I4D, 1I4L, 1I4T


• PubMed Abstract: 
  

Small G proteins are GTP-dependent molecular switches that regulate numerous cellular functions. They can be classified into homologous subfamilies that are broadly associated with specific biological processes. Cross-talk between small G-protein families has an important role in signalling, but the mechanism by which it occurs is poorly understood. The coordinated action of Arf and Rho family GTPases is required to regulate many cellular processes including lipid signalling, cell motility and Golgi function. Arfaptin is a ubiquitously expressed protein implicated in mediating cross-talk between Rac (a member of the Rho family) and Arf small GTPases. Here we show that Arfaptin binds specifically to GTP-bound Arf1 and Arf6, but binds to Rac.GTP and Rac.GDP with similar affinities. The X-ray structure of Arfaptin reveals an elongated, crescent-shaped dimer of three-helix coiled-coils. Structures of Arfaptin with Rac bound to either GDP or the slowly hydrolysable analogue GMPPNP show that the switch regions adopt similar conformations in both complexes. Our data highlight fundamental differences between the molecular mechanisms of Rho and Ras family signalling, and suggest a model of Arfaptin-mediated synergy between the Arf and Rho family signalling pathways.

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Organizational Affiliation: 

Division of Protein Structure, National Institute for Medical Research, Mill Hill, London NW7 IAA, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARFAPTIN 2	A, B	224	Homo sapiens	Mutation(s): 0  Gene Names: ARFIP2, POR1
UniProt & NIH Common Fund Data Resources
Find proteins for P53365 (Homo sapiens) Explore P53365  Go to UniProtKB:  P53365
PHAROS:  P53365

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1	C [auth D]	192	Homo sapiens	Mutation(s): 0  Gene Names: RAC1, TC25, MIG5 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63000 (Homo sapiens) Explore P63000  Go to UniProtKB:  P63000
PHAROS:  P63000

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
GDP	Binding MOAD:  1I4D	Kd: 3000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.298 
• R-Value Work: 0.238 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.566	α = 90
b = 47.462	β = 97.51
c = 125.311	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-02-20 
• Released Date: 2001-05-16 
Deposition Author(s): Tarricone, C., Xiao, B., Justin, N., Gamblin, S.J., Smerdon, S.J.

Revision History  

• Version 1.0: 2001-05-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Advisory, Data collection