3LVR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

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

  • 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 Arf ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3, ADP-ribosylation factor 6 E497Homo sapienssynthetic constructMutation(s): 0 
Gene Names: ASAP3ARF6
Find proteins for P62330 (Homo sapiens)
Explore P62330 
Go to UniProtKB:  P62330
NIH Common Fund Data Resources
PHAROS:  P62330
Find proteins for Q8TDY4 (Homo sapiens)
Explore Q8TDY4 
Go to UniProtKB:  Q8TDY4
NIH Common Fund Data Resources
PHAROS:  Q8TDY4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
E
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
AF3
Query on AF3

Download Ideal Coordinates CCD File 
E
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.45α = 90
b = 146.45β = 90
c = 49.62γ = 120
Software Package:
Software NamePurpose
ProDCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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