Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 55482.90 
• Atom Count: 3292 
• Residue Count: 497 
• Unique protein chains: 1

3LVR

The crystal structure of ASAP3 in complex with Arf6 in transition state soaked with Calcium

• DOI: 10.2210/pdb3LVR/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2010-02-22 Released: 2010-06-09 
• Deposition Author(s): Ismail, S.A., Vetter, I.R., Sot, B., Wittinghofer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.38 Å
• R-Value Free: 0.281 
• R-Value Work: 0.207 

Literature

The structure of an Arf-ArfGAP complex reveals a Ca2+ regulatory mechanism

Ismail, S.A., Vetter, I.R., Sot, B., Wittinghofer, A.

(2010) Cell 141: 812-821

• PubMed: 20510928 
• DOI: 10.1016/j.cell.2010.03.051
• Primary Citation of Related Structures:  
  3LVQ


• PubMed Abstract: 
  

Arfs are small G proteins that have a key role in vesicle trafficking and cytoskeletal remodeling. ArfGAP proteins stimulate Arf intrinsic GTP hydrolysis by a mechanism that is still unresolved. Using a fusion construct we solved the structure of the ArfGAP ASAP3 in complex with Arf6 in the transition state. This structure clarifies the ArfGAP catalytic mechanism and shows a glutamine((Arf6)) and an arginine finger((ASAP3)) as the important catalytic residues. Unexpectedly the structure shows a calcium ion, liganded by both proteins in the complex interface, stabilizing the interaction and orienting the catalytic machinery. Calcium stimulates the GAP activity of ASAPs, but not other members of the ArfGAP family. This type of regulation is unique for GAPs and any other calcium-regulated processes and hints at a crosstalk between Ca(2+) and Arf signaling.

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Organizational Affiliation: 

Department of Structural Biology, Max-Planck-Institute für Molekulare Physiologie, Dortmund 44227, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3, ADP-ribosylation factor 6	E	497	Homo sapiens	Mutation(s): 0  Gene Names: ASAP3 (DDEFL1, UPLC1), ARF6
Find proteins for Q8TDY4 (Homo sapiens) Go to Gene View: ASAP3 Go to UniProtKB:  Q8TDY4
Find proteins for P62330 (Homo sapiens) Go to Gene View: ARF6 Go to UniProtKB:  P62330

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GDP	E	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN	E	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	E	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	E	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
AF3	E	ALUMINUM FLUORIDE Al F3 KLZUFWVZNOTSEM-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.38 Å
• R-Value Free: 0.281 
• R-Value Work: 0.207 
• Space Group: P 6₂

Unit Cell:

Length (Å)	Angle (°)
a = 146.450	α = 90.00
b = 146.450	β = 90.00
c = 49.620	γ = 120.00

Software Package:

Software Name	Purpose
ProDC	data collection
REFMAC	refinement
MOLREP	phasing
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-22 
• Released Date: 2010-06-09 
• Deposition Author(s): Ismail, S.A., Vetter, I.R., Sot, B., Wittinghofer, A.

Revision History 

• Version 1.0: 2010-06-09
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-08-09
  Type: Refinement description, Source and taxonomy
• Version 1.3: 2017-11-08
  Type: Refinement description