1ABR

CRYSTAL STRUCTURE OF ABRIN-A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

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: 354-367

  • DOI: 10.1006/jmbi.1995.0382
  • Primary Citation of Related Structures:  
    1ABR

  • PubMed Abstract: 
  • The crystal structure of abrin-a, a type II ribosome-inactivating protein from the seeds of Abrus precatorius, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of ricin. The structure has been refined at 2 ...

    The crystal structure of abrin-a, a type II ribosome-inactivating protein from the seeds of Abrus precatorius, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of ricin. The structure has been refined at 2.14 A to a R-factor of 18.9%. The root-mean-square deviations of bond lengths and angles from the standard values are 0.013 A and 1.82 degrees, respectively. The overall protein folding is similar to that of ricin, but there are differences in the secondary structure, mostly of the A-chain. Several parts of the molecular surface differ significantly; some of them are quite near the active site cleft, and probably influence ribosome recognition. The positions of invariant active site residues remain the same, except the position of Tyr74. Two water molecules of hydrogen-bonded active site residues have been located in the active site cleft. Both of them may be responsible for hydrolyzing the N-C glycosidic bond. The current abrin-a structure is lactose free; this is probably essential for abrin-a crystallization. The B-chain is a glycoprotein, and the positions of several sugar residues of two sugar chains linked to earlier predicted glycosylation sites were determined. One of the sugar chains is a bridge between two neighboring molecules, since one of its mannose residues is connected to the galactose binding site of the neighboring molecule. Another sugar chain covers the surface of the B-chain.


    Related Citations: 
    • A New Crystal Form of Abrin-A from the Seeds of Abrus Precatorius
      Tahirov, T.H., Lu, T.-H., Liaw, Y.-C., Chu, S.-C., Lin, J.-Y.
      (1994) J Mol Biol 235: 1152
    • Primary Structure of Three Distinct Isobrins Determined by Cdna Sequencing: Conservation and Significance
      Hung, C.-H., Lee, M.-C., Lee, T.-C., Lin, J.-Y.
      (1993) J Mol Biol 229: 263
    • The Complete Amino Acid Sequence of the A-Chain of Abrin-1, a Toxic Protein from the Seeds of Abrus Precatorius
      Fanatsu, G., Taguchi, Y., Kamenosono, M., Yanaka, M.
      (1988) J Biol Chem 52: 1095

    Organizational Affiliation

    Department of Physics, National Tsing Hua University, Hsinchu, Taiwan, Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ABRIN-A A251Abrus precatoriusMutation(s): 0 
EC: 3.2.2.22
Find proteins for P11140 (Abrus precatorius)
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Go to UniProtKB:  P11140
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ABRIN-A B267N/AMutation(s): 0 
Find proteins for P11140 (Abrus precatorius)
Explore P11140 
Go to UniProtKB:  P11140
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-L-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose
C
5 N/A Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose
D
5 N/A Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.58α = 90
b = 73.07β = 96.2
c = 48.23γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-02-07
    Type: Initial release
  • Version 1.1: 2008-03-10
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary