1IOO

CRYSTAL STRUCTURE OF NICOTIANA ALATA GEMETOPHYTIC SELF-INCOMPATIBILITY ASSOCIATED SF11-RNASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.185 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The 1.55 A resolution structure of Nicotiana alata S(F11)-RNase associated with gametophytic self-incompatibility.

Ida, K.Norioka, S.Yamamoto, M.Kumasaka, T.Yamashita, E.Newbigin, E.Clarke, A.E.Sakiyama, F.Sato, M.

(2001) J Mol Biol 314: 103-112

  • DOI: 10.1006/jmbi.2001.5127
  • Primary Citation of Related Structures:  
    1IOO

  • PubMed Abstract: 
  • The crystal structure of Nicotiana alata (ornamental tobacco) S(F11)-RNase, an S-allelic glycoprotein associated with gametophytic self-incompatibility, was determined by X-ray diffraction at 1.55 A resolution. The protein has a tertiary structure typical of members of the RNase T(2) family as it consists of a variant of the (alpha+beta) fold and has eight helices and seven strands ...

    The crystal structure of Nicotiana alata (ornamental tobacco) S(F11)-RNase, an S-allelic glycoprotein associated with gametophytic self-incompatibility, was determined by X-ray diffraction at 1.55 A resolution. The protein has a tertiary structure typical of members of the RNase T(2) family as it consists of a variant of the (alpha+beta) fold and has eight helices and seven strands. A heptasaccharide moiety is also present, and amino acid residues that serve as the catalytic acid and base can be assigned to His32 and His91, respectively. Two "hypervariable" regions, known as HVa and HVb, are the proposed sites of S-allele discrimination during the self-incompatibility reaction, and in the S(F11)-RNase these are well separated from the active site. HVa and HVb are composed of a long, positively charged loop followed by a part of an alpha-helix and short, negatively charged alpha-helix, respectively. The S(F11)-RNase structure shows both regions are readily accessible to the solvent and hence could participate in the process of self/non-self discrimination between the S-RNase and an unknown pollen S-gene product(s) upon pollination.


    Organizational Affiliation

    Graduate School of Integrated Science, Yokohama City University, Tsurumi-ku, Yokohama 230-0045, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SF11-RNASEA, B196Nicotiana alataMutation(s): 0 
EC: 4.6.1.19
UniProt
Find proteins for Q7SID5 (Nicotiana alata)
Explore Q7SID5 
Go to UniProtKB:  Q7SID5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SID5
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D 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)-2-acetamido-2-deoxy-beta-D-glucopyranoseC 5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G78255UI
GlyCosmos:  G78255UI
GlyGen:  G78255UI
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-xylopyranose-(1-2)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD 7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G32473MI
GlyCosmos:  G32473MI
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.869α = 90
b = 44.731β = 90.27
c = 64.36γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary