1HWO

EBULIN COMPLEXED WITH LACTOSE, TRIGONAL CRYSTAL FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

2.8-A crystal structure of a nontoxic type-II ribosome-inactivating protein, ebulin l.

Pascal, J.M.Day, P.J.Monzingo, A.F.Ernst, S.R.Robertus, J.D.Iglesias, R.Perez, Y.Ferreras, J.M.Citores, L.Girbes, T.

(2001) Proteins 43: 319-326

  • Primary Citation of Related Structures:  1HWM, 1HWN, 1HWP

  • PubMed Abstract: 
  • Ebulin l is a type-II ribosome-inactivating protein (RIP) isolated from the leaves of Sambucus ebulus L. As with other type-II RIP, ebulin is a disulfide-linked heterodimer composed of a toxic A chain and a galactoside-specific lectin B chain. A norm ...

    Ebulin l is a type-II ribosome-inactivating protein (RIP) isolated from the leaves of Sambucus ebulus L. As with other type-II RIP, ebulin is a disulfide-linked heterodimer composed of a toxic A chain and a galactoside-specific lectin B chain. A normal level of ribosome-inactivating N-glycosidase activity, characteristic of the A chain of type-II RIP, has been demonstrated for ebulin l. However, ebulin is considered a nontoxic type-II RIP due to a reduced cytotoxicity on whole cells and animals as compared with other toxic type-II RIP like ricin. The molecular cloning, amino acid sequence, and the crystal structure of ebulin l are presented and compared with ricin. Ebulin l is shown to bind an A-chain substrate analogue, pteroic acid, in the same manner as ricin. The galactoside-binding ability of ebulin l is demonstrated crystallographically with a complex of the B chain with galactose and with lactose. The negligible cytotoxicity of ebulin l is apparently due to a reduced affinity for galactosides. An altered mode of galactoside binding in the 2gamma subdomain of the lectin B chain primarily causes the reduced affinity.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EBULIN
A
254Sambucus ebulusGene Names: ebu1
EC: 3.2.2.22
Find proteins for Q9AVR2 (Sambucus ebulus)
Go to UniProtKB:  Q9AVR2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
EBULIN
B
266Sambucus ebulusGene Names: ebu1
EC: 3.2.2.22
Find proteins for Q9AVR2 (Sambucus ebulus)
Go to UniProtKB:  Q9AVR2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL
Query on GAL

Download SDF File 
Download CCD File 
B
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
B
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.237 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.000α = 90.00
b = 74.000β = 90.00
c = 191.500γ = 120.00
Software Package:
Software NamePurpose
EPMRphasing
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description