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(-) Description

Title :  CRYSTAL STRUCTURE OF THE STRAWBERRY PATHOGENESIS-RELATED 10 (PR-10) FRA A 3 PROTEIN IN COMPLEX WITH CATECHIN
 
Authors :  A. Casanal, U. Zander, V. Valpuesta, J. A. Marquez
Date :  02 Oct 13  (Deposition) - 16 Oct 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Keywords :  Allergen, Pyr/Pyl/Rcar, Bet V 1, Flavonoids (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Casanal, U. Zander, C. Munoz, F. Dupeux, I. Luque, M. A. Botella, W. Schwab, V. Valpuesta, J. A. Marquez
The Strawberry Pathogenesis-Related 10 (Pr-10) Fra A Proteins Control Flavonoid Biosynthesis By Binding To Metabolic Intermediates.
J. Biol. Chem. V. 288 35322 2013
PubMed-ID: 24133217  |  Reference-DOI: 10.1074/JBC.M113.501528
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRA A 3 ALLERGEN
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PETM11
    Expression System Vector Type: PLASMID
    Organism Common: STRAWBERRY
    Organism Scientific: FRAGARIA X ANANASSA
    Organism Taxid: 3747

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A    
Biological Unit 2 (1x):  B   
Biological Unit 3 (1x):   C  
Biological Unit 4 (1x):    D 
Biological Unit 5 (1x):     E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1KXN6Ligand/Ion(2R,3S)-2-(3,4-DIHYDROXYPHENYL)-3,4-DIHYDRO-2H-CHROMENE-3,5,7-TRIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1KXN1Ligand/Ion(2R,3S)-2-(3,4-DIHYDROXYPHENYL)-3,4-DIHYDRO-2H-CHROMENE-3,5,7-TRIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1KXN1Ligand/Ion(2R,3S)-2-(3,4-DIHYDROXYPHENYL)-3,4-DIHYDRO-2H-CHROMENE-3,5,7-TRIOL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1KXN1Ligand/Ion(2R,3S)-2-(3,4-DIHYDROXYPHENYL)-3,4-DIHYDRO-2H-CHROMENE-3,5,7-TRIOL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1KXN1Ligand/Ion(2R,3S)-2-(3,4-DIHYDROXYPHENYL)-3,4-DIHYDRO-2H-CHROMENE-3,5,7-TRIOL
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1KXN2Ligand/Ion(2R,3S)-2-(3,4-DIHYDROXYPHENYL)-3,4-DIHYDRO-2H-CHROMENE-3,5,7-TRIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:59 , SER A:63 , HIS A:70 , ASP A:90 , ARG A:139 , HOH A:2001 , HOH A:2002 , HOH A:2004 , HOH A:2005BINDING SITE FOR RESIDUE KXN A 160
2AC2SOFTWAREILE B:31 , HIS B:70 , ARG B:139 , HOH B:2001BINDING SITE FOR RESIDUE KXN B 160
3AC3SOFTWAREILE C:57 , LEU C:59 , HIS C:70 , ARG C:139 , HOH C:2001 , HOH C:2002BINDING SITE FOR RESIDUE KXN C 160
4AC4SOFTWAREPHE D:23 , LEU D:59 , HIS D:70 , ARG D:139 , HOH D:2001 , HOH D:2002BINDING SITE FOR RESIDUE KXN D 160
5AC5SOFTWAREASP E:28 , ALA E:38 , LEU E:59 , SER E:63 , HIS E:70 , ARG E:139 , LEU E:143 , HOH E:2001BINDING SITE FOR RESIDUE KXN E 160
6AC6SOFTWAREPRO A:32 , LYS A:33 , PRO A:36 , LYS A:40 , PHE B:10 , THR B:11 , LYS B:145 , LYS E:40 , GLU E:61 , GLY E:62 , HOH E:2002BINDING SITE FOR RESIDUE KXN E 161

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C94)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly E:60 -Glu E:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C94)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C94)

(-) Exons   (0, 0)

(no "Exon" information available for 4C94)

(-) Sequences/Alignments

Asymmetric Unit
   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:161
 aligned with D0E0C7_FRAAN | D0E0C7 from UniProtKB/TrEMBL  Length:159

    Alignment length:161
                              1                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
         D0E0C7_FRAAN     - --MGVFTYESEFTSVIPPPKLFKAFVLDADNLIPKIAPQAVKSAEIIEGDGGVGTIKKIHLGEGSEYSYVKHKIDGIDKDNFVYSYSIIEGDAIGDKIEKISYEIKLVASGGGSIIKSTSHYHTKGEVEIKEEHVKAGKERAAGLFKIIENHLLAHPEEYN 159
               SCOP domains d4c94a_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee..hhhhhhhhhh.hhhhhhhhhh...eeeeeeee.......eeeeee.hhhh..eeeeeeeeee....eeeeeeeee......eeeeeeeeeeee....eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c94 A  -1 AMAGVFTYESEFTSVIPPPKLFKAFVLDADNLIPKIAPQAVKSAEIIEGDGGVGTIKKIHLGEGSEYSYVKHKIDGIDKDNFVYSYSIIEGDAIGDKIEKISYEIKLVASGGGSIIKSTSHYHTKGEVEIKEEHVKAGKERAAGLFKIIENHLLAHPEEYN 159
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with D0E0C7_FRAAN | D0E0C7 from UniProtKB/TrEMBL  Length:159

    Alignment length:161
                              1                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
         D0E0C7_FRAAN     - --MGVFTYESEFTSVIPPPKLFKAFVLDADNLIPKIAPQAVKSAEIIEGDGGVGTIKKIHLGEGSEYSYVKHKIDGIDKDNFVYSYSIIEGDAIGDKIEKISYEIKLVASGGGSIIKSTSHYHTKGEVEIKEEHVKAGKERAAGLFKIIENHLLAHPEEYN 159
               SCOP domains d4c94b_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..hhhhhhhhhh.hhhhhhhhhh...eeeeee.........eeeeee.hhhh..eeeeeeeeee....eeeeeeee.......eeeeeeeeeeeee..eeeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c94 B  -1 AMAGVFTYESEFTSVIPPPKLFKAFVLDADNLIPKIAPQAVKSAEIIEGDGGVGTIKKIHLGEGSEYSYVKHKIDGIDKDNFVYSYSIIEGDAIGDKIEKISYEIKLVASGGGSIIKSTSHYHTKGEVEIKEEHVKAGKERAAGLFKIIENHLLAHPEEYN 159
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 


Chain C from PDB  Type:PROTEIN  Length:161
 aligned with D0E0C7_FRAAN | D0E0C7 from UniProtKB/TrEMBL  Length:159

    Alignment length:161
                              1                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
         D0E0C7_FRAAN     - --MGVFTYESEFTSVIPPPKLFKAFVLDADNLIPKIAPQAVKSAEIIEGDGGVGTIKKIHLGEGSEYSYVKHKIDGIDKDNFVYSYSIIEGDAIGDKIEKISYEIKLVASGGGSIIKSTSHYHTKGEVEIKEEHVKAGKERAAGLFKIIENHLLAHPEEYN 159
               SCOP domains d4c94c_ C: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..hhhhhhhhhh.hhhhhhhhhh.......eee........eeeee........eeeeeeeeee....eeeeee.........eeeeeeeeeeeee..eeeeeeeeeeeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c94 C  -1 AMAGVFTYESEFTSVIPPPKLFKAFVLDADNLIPKIAPQAVKSAEIIEGDGGVGTIKKIHLGEGSEYSYVKHKIDGIDKDNFVYSYSIIEGDAIGDKIEKISYEIKLVASGGGSIIKSTSHYHTKGEVEIKEEHVKAGKERAAGLFKIIENHLLAHPEEYN 159
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 


Chain D from PDB  Type:PROTEIN  Length:156
 aligned with D0E0C7_FRAAN | D0E0C7 from UniProtKB/TrEMBL  Length:159

    Alignment length:161
                              1                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
         D0E0C7_FRAAN     - --MGVFTYESEFTSVIPPPKLFKAFVLDADNLIPKIAPQAVKSAEIIEGDGGVGTIKKIHLGEGSEYSYVKHKIDGIDKDNFVYSYSIIEGDAIGDKIEKISYEIKLVASGGGSIIKSTSHYHTKGEVEIKEEHVKAGKERAAGLFKIIENHLLAHPEEYN 159
               SCOP domains d4c94d_ D: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..hhhhhhhhhh.hhhhhhhhhh.......eee........eeeee..-----.eeeeeeeeee....eeeeeeeee......eeeeeeeeeeeee..eeeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c94 D  -1 AMAGVFTYESEFTSVIPPPKLFKAFVLDADNLIPKIAPQAVKSAEIIEGDGGVGTIKKIHLG-----SYVKHKIDGIDKDNFVYSYSIIEGDAIGDKIEKISYEIKLVASGGGSIIKSTSHYHTKGEVEIKEEHVKAGKERAAGLFKIIENHLLAHPEEYN 159
                                     8        18        28        38        48        58 |     |68        78        88        98       108       118       128       138       148       158 
                                                                                        60    66                                                                                             


Chain E from PDB  Type:PROTEIN  Length:161
 aligned with D0E0C7_FRAAN | D0E0C7 from UniProtKB/TrEMBL  Length:159

    Alignment length:161
                              1                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
         D0E0C7_FRAAN     - --MGVFTYESEFTSVIPPPKLFKAFVLDADNLIPKIAPQAVKSAEIIEGDGGVGTIKKIHLGEGSEYSYVKHKIDGIDKDNFVYSYSIIEGDAIGDKIEKISYEIKLVASGGGSIIKSTSHYHTKGEVEIKEEHVKAGKERAAGLFKIIENHLLAHPEEYN 159
               SCOP domains d4c94e_ E: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee..hhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......eeeeee.......eeeeeeeeee....eeeeeeeee......eeeeeeeeeeeee..eeeeeeeeeeee...eeehhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c94 E  -1 AMAGVFTYESEFTSVIPPPKLFKAFVLDADNLIPKIAPQAVKSAEIIEGDGGVGTIKKIHLGEGSEYSYVKHKIDGIDKDNFVYSYSIIEGDAIGDKIEKISYEIKLVASGGGSIIKSTSHYHTKGEVEIKEEHVKAGKERAAGLFKIIENHLLAHPEEYN 159
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158
   Legend:   → Mismatch (orange background)
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  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, 5)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C94)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C94)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (D0E0C7_FRAAN | D0E0C7)
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:0009607    response to biotic stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism.

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  4c94
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 Related Entries

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