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(-) Description

Title :  DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF RAPHANUS SATIVUS ANTIFUNGAL PROTEIN 1 (RS-AFP1) BY 1H NMR, 20 STRUCTURES
 
Authors :  F. Fant, F. A. M. Borremans
Date :  05 Nov 97  (Deposition) - 28 Jan 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Fungicide, Plant Defensin, Cysteine-Stabilized Alfa/Beta Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Fant, W. Vranken, W. Broekaert, F. Borremans
Determination Of The Three-Dimensional Solution Structure Of Raphanus Sativus Antifungal Protein 1 By 1H Nmr.
J. Mol. Biol. V. 279 257 1998
PubMed-ID: 9636715  |  Reference-DOI: 10.1006/JMBI.1998.1767
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTIFUNGAL PROTEIN 1
    Chains: A
    Organ: SEED
    Organism Common: CHINESE RADISH
    Organism Scientific: RAPHANUS SATIVUS VAR. NIGER
    Organism Taxid: 41679
    Strain: VAR. NIGER
    Synonym: RS-AFP1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 1AYJ)

(-) SS Bonds  (4, 4)

NMR Structure
No.Residues
1A:4 -A:51
2A:15 -A:36
3A:21 -A:45
4A:25 -A:47

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Phe A:40 -Pro A:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AYJ)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAMMA_THIONINPS00940 Gamma-thionins family signature.DEF1_SINAL2-25  1A:2-25
DEF1_RAPSA31-54  1A:2-25

(-) Exons   (0, 0)

(no "Exon" information available for 1AYJ)

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:51
 aligned with DEF1_RAPSA | P69241 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:51
                                    39        49        59        69        79 
            DEF1_RAPSA   30 QKLCERPSGTWSGVCGNNNACKNQCINLEKARHGSCNYVFPAHKCICYFPC 80
               SCOP domains d1ayja_ A: Antifungal protein 1 (RS-AFP1)           SCOP domains
               CATH domains -1ayjA00 A:2-51  [code=3.30.30.10, no name defined] CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........hhhhhhhhhhh....eeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE -GAMMA_THIONIN           -------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                  1ayj A  1 xKLCERPSGTWSGVCGNNNACKNQCINLEKARHGSCNYVFPAHKCICYFPC 51
                            |       10        20        30        40        50 
                            |                                                  
                            1-PCA                                              


Chain A from PDB  Type:PROTEIN  Length:51
 aligned with DEF1_SINAL | P30231 from UniProtKB/Swiss-Prot  Length:51

    Alignment length:51
                                    10        20        30        40        50 
            DEF1_SINAL    1 QKLCERPSGTWSGVCGNNNACKNQCINLEKARHGSCNYVFPAHKCICYFPC 51
               SCOP domains d1ayja_ A: Antifungal protein 1 (RS-AFP1)           SCOP domains
               CATH domains -1ayjA00 A:2-51  [code=3.30.30.10, no name defined] CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........hhhhhhhhhhh....eeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE -GAMMA_THIONIN           -------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                  1ayj A  1 xKLCERPSGTWSGVCGNNNACKNQCINLEKARHGSCNYVFPAHKCICYFPC 51
                            |       10        20        30        40        50 
                            1-PCA
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AYJ)

(-) Gene Ontology  (4, 7)

NMR Structure(hide GO term definitions)
Chain A   (DEF1_SINAL | P30231)
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.

Chain A   (DEF1_RAPSA | P69241)
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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    Phe A:40 - Pro A:41   [ RasMol ]  
 

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