2ERP

Crystal structure of vascular apoptosis-inducing protein-1(inhibitor-bound form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of VAP1 reveal ADAMs' MDC domain architecture and its unique C-shaped scaffold

Takeda, S.Igarashi, T.Mori, H.Araki, S.

(2006) Embo J. 25: 2388-2396

  • DOI: 10.1038/sj.emboj.7601131
  • Primary Citation of Related Structures:  
  • Also Cited By: 2DW2, 2DW1, 2DW0

  • PubMed Abstract: 
  • ADAMs (a disintegrin and metalloproteinase) are sheddases possessing extracellular metalloproteinase/disintegrin/cysteine-rich (MDC) domains. ADAMs uniquely display both proteolytic and adhesive activities on the cell surface, however, most of their ...

    ADAMs (a disintegrin and metalloproteinase) are sheddases possessing extracellular metalloproteinase/disintegrin/cysteine-rich (MDC) domains. ADAMs uniquely display both proteolytic and adhesive activities on the cell surface, however, most of their physiological targets and adhesion mechanisms remain unclear. Here for the first time, we reveal the ADAMs' MDC architecture and a potential target-binding site by solving crystal structures of VAP1, a snake venom homolog of mammalian ADAMs. The D-domain protrudes from the M-domain opposing the catalytic site and constituting a C-shaped arm with cores of Ca2+ ions. The disintegrin-loop, supposed to interact with integrins, is packed by the C-domain and inaccessible for protein binding. Instead, the hyper-variable region (HVR) in the C-domain, which has a novel fold stabilized by the strictly conserved disulfide bridges, constitutes a potential protein-protein adhesive interface. The HVR is located at the distal end of the arm and faces toward the catalytic site. The C-shaped structure implies interplay between the ADAMs' proteolytic and adhesive domains and suggests a molecular mechanism for ADAMs' target recognition for shedding.


    Related Citations: 
    • Crystallization and preliminary X-ray crystallographic analysis of two vascular apoptosis-inducing proteins (VAPs) from Crotalus atrox venom
      Igarashi, T.,Oishi, Y.,Araki, S.,Mori, H.,Takeda, S.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Cardiac Physiology, National Cardiovascular Center Research Institute, Suita, Osaka, Japan. stakeda@ri.ncvc.go.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
vascular apoptosis-inducing protein 1
A, B
427Crotalus atroxMutation(s): 0 
EC: 3.4.24.-
Find proteins for Q9DGB9 (Crotalus atrox)
Go to UniProtKB:  Q9DGB9
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
3CO
Query on 3CO

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Download CCD File 
A
COBALT (III) ION
Co
JAWGVVJVYSANRY-UHFFFAOYSA-N
 Ligand Interaction
GM6
Query on GM6

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Download CCD File 
A, B
3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE
GM6001
C20 H28 N4 O4
NITYDPDXAAFEIT-DYVFJYSZSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.345α = 90.00
b = 91.379β = 90.00
c = 136.039γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance