1CF5

BETA-MOMORCHARIN STRUCTURE AT 2.55 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report



Literature

Three-dimensional structure of beta-momorcharin at 2.55 A resolution.

Yuan, Y.R.He, Y.N.Xiong, J.P.Xia, Z.X.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1144-1151

  • DOI: 10.1107/s0907444999003297
  • Primary Citation of Related Structures:  
    1CF5

  • PubMed Abstract: 
  • Beta-Momorcharin (Mr approximately 29 kDa) is a single-chained ribosome-inactivating protein (RIP) with a branched hexasaccharide bound to Asn51. The crystal structure of beta-momorcharin has been determined using the molecular-replacement method and ref ...

    Beta-Momorcharin (Mr approximately 29 kDa) is a single-chained ribosome-inactivating protein (RIP) with a branched hexasaccharide bound to Asn51. The crystal structure of beta-momorcharin has been determined using the molecular-replacement method and refined to 2. 55 A resolution. The final structural model gave an R factor of 17. 2% and root-mean-square deviations of 0.016 A and 1.76 degrees from ideal bond lengths and bond angles, respectively. beta-Momorcharin contains nine alpha-helices, two 310 helices and three beta-sheets, and its overall structure is similar to those of other single-chained RIPs. Residues Tyr70, Tyr109, Glu158 and Arg161 are expected to define the active site of beta-momorcharin as an rRNA N-glycosidase. The oligosaccharide is linked to the protein through an N-glycosidic bond, beta-GlcNAc-(1-N)-Asn51, and stretches from the surface of the N-terminal domain far from the active site, which suggests that it should not play a role in enzymatic function. The oligosaccharide of each beta-momorcharin molecule interacts with the protein through hydrogen bonds, although in the crystals most of these are intermolecular interactions with the protein atoms in an adjacent unit cell. This is the first example of an RIP structure which provides information about the three-dimensional structure and binding site of the oligosaccharide in the active chains of RIPs.


    Related Citations: 
    • The Determination and Refinement of Three-Dimensional Structure of Beta- Momorcharin at 2.4 A Resolution
      Yuan, Y.-R., Xiong, J.-P., Xia, Z.-X.
      (1995) Chin Chem Lett 6: 1053
    • Crystallization and preliminary crystallographic study of beta-momorcharin.
      Xiong, J.P., Xia, Z.X., Zhang, L., Ye, G.J., Jin, S.W., Wang, Y.
      (1994) J Mol Biol 238: 284

    Organizational Affiliation

    Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (BETA-MOMORCHARIN) AB249Momordica charantiaMutation(s): 0 
Gene Names: MAP30RIP
EC: 3.2.2.22
Find proteins for P24817 (Momordica charantia)
Explore P24817 
Go to UniProtKB:  P24817
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.09α = 72.98
b = 50.58β = 78.39
c = 61.12γ = 76.97
Software Package:
Software NamePurpose
MERLOTphasing
X-PLORrefinement
X-GENdata reduction
X-GENdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-07
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2019-11-13
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary