Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 60.06 kDa 
• Atom Count: 4411 
• Residue Count: 518 
• Unique protein chains: 2

1ABR

CRYSTAL STRUCTURE OF ABRIN-A

• DOI: 10.2210/pdb1ABR/pdb

• Classification: GLYCOSIDASE/CARBOHYDRATE
• Organism(s): Abrus precatorius
• Mutation(s): No 


• Deposited: 1994-11-11 Released: 1995-02-07 
• Deposition Author(s): Tahirov, T.H., Lu, T.-H., Liaw, Y.-C., Chu, S.-C., Lin, J.-Y.

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Experimental Data Snapshot

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

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

• PubMed: 7608980 
• 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 2.14 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABRIN-A	A	251	Abrus precatorius	Mutation(s): 0  EC: 3.2.2.22
Find proteins for P11140 (Abrus precatorius) Explore P11140  Go to UniProtKB:  P11140

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ABRIN-A	B	267	N/A	Mutation(s): 0
Find proteins for P11140 (Abrus precatorius) Explore P11140  Go to UniProtKB:  P11140

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram
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

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram
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

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 = 84.58	α = 90
b = 73.07	β = 96.2
c = 48.23	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-11-11 
• Released Date: 1995-02-07 
Deposition Author(s): Tahirov, T.H., Lu, T.-H., Liaw, Y.-C., Chu, S.-C., Lin, J.-Y.

Revision History 

• 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