2ZR1

Agglutinin from Abrus Precatorius


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A biophysical elucidation for less toxicity of Agglutinin than Abrin-a from the Seeds of Abrus Precatorius in consequence of crystal structure

Cheng, J.Lu, T.H.Liu, C.L.Lin, J.Y.

(2010) J.Biomed.Sci. 17: 34-34

  • DOI: 10.1186/1423-0127-17-34

  • PubMed Abstract: 
  • X-ray crystal structure determination of agglutinin from Abrus precatorius in Taiwan is presented. The crystal structure of agglutinin, a type II ribosome-inactivating protein (RIP) from the seeds of Abrus precatorius in Taiwan, has been determined f ...

    X-ray crystal structure determination of agglutinin from Abrus precatorius in Taiwan is presented. The crystal structure of agglutinin, a type II ribosome-inactivating protein (RIP) from the seeds of Abrus precatorius in Taiwan, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of abrin-a as the template. The structure has space group P4(1)2(1)2 with Z = 8, and been refined at 2.6 A to R-factor of 20.4%. The root-mean-square deviations of bond lengths and angles from the standard values are 0.009 A and 1.3 degrees. Primary, secondary, tertiary and quaternary structures of agglutinin have been described and compared with those of abrin-a to a certain extent. In subsequent docking research, we found that Asn200 of abrin-a may form a critical hydrogen bond with G4323 of 28SRNA, while corresponding Pro199 of agglutinin is a kink hydrophobic residue bound with the cleft in a more compact complementary relationship. This may explain the lower toxicity of agglutinin than abrin-a, despite of similarity in secondary structure and the activity cleft of two RIPs.


    Related Citations: 
    • Structure-function analysis and insights into the reduced toxicity of Abrus precatorius agglutinin I in relation to abrin
      Bagaria, A.,Surendranath, K.,Ramagopal, U.A.,Ramakumar, S.,Karande, A.A.
      (2006) J.Biol.Chem. 281: 34465
    • Crystal structure of abrin-a at 2.14 A
      Tahirov, T.H.,Lu, T.-H.,Liaw, Y.-C.,Chen, Y.-L.,Lin, J.-Y.
      (1995) J.Mol.Biol. 250: 354
    • Crystallization of agglutinin from the seeds of Abrus precatorius
      Panneerselvam, K.,Lin, S.-C.,Liu, C.-L.,Liaw, Y.-C.,Lin, J.-Y.,Lu, T.-H.
      (2000) Acta Crystallogr.,Sect.D 56: 898
    • Primary structure and function analysis of the Abrus precatorius agglutinin A chain by site-directed mutagenesis. Pro(199) Of amphiphilic alpha-helix H impairs protein synthesis inhibitory activity
      Liu, C.-L.,Tsai, C.-C.,Lin, S.-C.,Wang, L.-I.,Hsu, C.-I.,Hwang, M.-J.,Lin, J.-Y.
      (2000) J.Biol.Chem. 275: 1897


    Organizational Affiliation

    Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Agglutinin-1 chain A
A, C
258Abrus precatoriusMutation(s): 0 
Gene Names: AAG
Find proteins for Q9M6E9 (Abrus precatorius)
Go to UniProtKB:  Q9M6E9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Agglutinin-1 chain B
B, D
267Abrus precatoriusMutation(s): 0 
Gene Names: AAG
Find proteins for Q9M6E9 (Abrus precatorius)
Go to UniProtKB:  Q9M6E9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
B
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 137.050α = 90.00
b = 137.050β = 90.00
c = 214.424γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-11
    Type: Refinement description
  • Version 1.3: 2019-10-16
    Type: Advisory, Data collection, Derived calculations