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(-) Description

Title :  CRYSTAL STRUCTURE OF POTATO RX-CC DOMAIN IN COMPLEX WITH RANGAP2-WPP DOMAIN
 
Authors :  J. Chai, W. Hao
Date :  12 Aug 13  (Deposition) - 13 Nov 13  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,E,H,I,J,K,L,Q,R
Biol. Unit 1:  A,R  (1x)
Biol. Unit 2:  E,L  (1x)
Biol. Unit 3:  I,J  (1x)
Biol. Unit 4:  B,H  (1x)
Biol. Unit 5:  K,Q  (1x)
Keywords :  Rx, Rangap2, Coiled Coil Domain, Wpp Domain, Plant Disease Resistance Gene, Resistance Responses, Popato X Virus, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Hao, S. M. Collier, P. Moffett, J. Chai
Structural Basis For The Interaction Between The Potato Virus X Resistance Protein (Rx) And Its Cofactor Ran Gtpase-Activating Protein 2 (Rangap2)
J. Biol. Chem. V. 288 35868 2013
PubMed-ID: 24194517  |  Reference-DOI: 10.1074/JBC.M113.517417

(-) Compounds

Molecule 1 - RX PROTEIN
    Chains: A, L, I, H, Q
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RX-CC DOMAIN, UNP RESIDUES 1-122
    Gene: RX
    Organism Common: POTATO
    Organism Scientific: SOLANUM TUBEROSUM
    Organism Taxid: 4113
 
Molecule 2 - RAN GTPASE ACTIVATING PROTEIN 2
    Chains: E, J, B, K
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: STRANGAP2-WPP DOMAIN, UNP RESIDUES 15-112
    Gene: RANGAP2
    Organism Common: POTATO
    Organism Scientific: SOLANUM TUBEROSUM
    Organism Taxid: 4113
 
Molecule 3 - RAN GTPASE ACTIVATING PROTEIN 2
    Chains: R
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: STRANGAP2-WPP DOMAIN, UNP RESIDUES 15-112
    Gene: RANGAP2, RX
    Organism Common: POTATO
    Organism Scientific: SYNTHETIC CONSTRUCT, SOLANUM TUBEROSUM
    Organism Taxid: 32630, 4113

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABEHIJKLQR
Biological Unit 1 (1x): A        R
Biological Unit 2 (1x):   E    L  
Biological Unit 3 (1x):     IJ    
Biological Unit 4 (1x):  B H      
Biological Unit 5 (1x):       K Q 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 27)

Asymmetric Unit (1, 27)
No.NameCountTypeFull Name
1UNK27Mod. Amino Acid
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1UNK-1Mod. Amino Acid
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1UNK-1Mod. Amino Acid
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1UNK-1Mod. Amino Acid
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1UNK-1Mod. Amino Acid
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1UNK-1Mod. Amino Acid

(-) Sites  (0, 0)

(no "Site" information available for 4M70)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M70)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Trp E:19 -Pro E:20
2Trp J:19 -Pro J:20
3Trp B:19 -Pro B:20
4Pro B:78 -Asp B:79
5Ala K:85 -Val K:86

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M70)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M70)

(-) Exons   (0, 0)

(no "Exon" information available for 4M70)

(-) 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:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 4m70 A  -1 GAMAYAAVTSLMRTIHQSMELTGCDLQPFYEKLKSLRAILELTILEVEIVEVAYTTEDMVDSESRNVFLAQNLEERSRAMWEIFFVLEQALECIDSTVKQWMATSDS 116
                                     8        18        28        38||      59        69        79        89        99       109       
                                                                   39|                                                                 
                                                                    51                                                                 


Chain B from PDB  Type:PROTEIN  Length:91
                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 4m70 B  15 AIKLWPPSENTRKMLVERMTNNLSSPTIFTRKYRSLSKEEAAKNAEEIEDAAFTIANQHYEKEPDGDGSSAVQLYARECSKLILEILKKIP 105
                                    24        34        44        54        64        74        84        94       104 


Chain E from PDB  Type:PROTEIN  Length:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4m70 E  16 IKLWPPSENTRKMLVERMTNNLSSPTIFTRKYRSLSKEEAAKNAEEIEDAAFTIANQHYEKEPDGDGSSAVQLYARECSKLILEILKK 103
                                    25        35        45        55        65        75        85        95        


Chain H from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 4m70 H  -2 AGAMAYAAVTSLMRTIHQSMELTGCDLQPFYEKLKSLRAILEHEGLTILEVEIVEVAYTTEDMVDSESRNVFLAQNLEERSRAMWEIFFVLEQALECIDSTVKQWMATSDSM 117
                                     7        17        27        37 ||     55        65        75        85        95       105       115  
                                                                    39|                                                                     
                                                                     48                                                                     


Chain I from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 4m70 I   0 AMAYAAVTSLMRTIHQSMELTGCDLQPFYEKLKSLRAILEKGLTILEVEIVEVAYTTEDMVDSESRNVFLAQNLEERSRAMWEIFFVLEQALECIDSTVKQWMATSDS 116
                                     9        19        29        39||      58        68        78        88        98       108        
                                                                   40|                                                                  
                                                                    50                                                                  


Chain J from PDB  Type:PROTEIN  Length:89
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 4m70 J  16 IKLWPPSENTRKMLVERMTNNLSSPTIFTRKYRSLSKEEAAKNAEEIEDAAFTIANQHYEKEPDGDGSSAVQLYARECSKLILEILKKI 104
                                    25        35        45        55        65        75        85        95         


Chain K from PDB  Type:PROTEIN  Length:56
                                                                                        
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 4m70 K  27 KMLVERMTNNLSSPTIFTRKEEAAKNAEEIEDAAFTIAVQLYARECSKLILEILKK 103
                                    36        46|       62      ||87        97      
                                              46|              69|                  
                                               53               85                  


Chain L from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 4m70 L  -3 AAGAMAYAAVTSLMRTIHQSMELTGCDLQPFYEKLKSLRAILEKEGLTILEVEIVEVAYTTEDMVDSESRNVFLAQNLEERSRAMWEIFFVLEQALECIDSTVKQWMATSDS 116
                                     6        16        26        36   ||   54        64        74        84        94       104       114  
                                                                      40|                                                                   
                                                                       49                                                                   


Chain Q from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 4m70 Q   0 AMAYAAVTSLMRTIHQSMELTGCDLQPFYEKLKSLRAILEEGLTILEVEIVEVAYTTEDMVDSESRNVFLAQNLEERSRAMWEIFFVLEQALECIDSTVKQWMATSDS 116
                                     9        19        29        39|       58        68        78        88        98       108        
                                                                  39|                                                                   
                                                                   49                                                                   


Chain R from PDB  Type:PROTEIN  Length:56
                                                                                        
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 4m70 R  23 xxxxxxxxxxxSSPTIFSKEEAAKNAEEIEDAAFTIANQHxxxxxxxxxxxxxxxx 101
                            ||||||||32||    ||53        63        73||||||||95||||||
                           23-UNK|||32-UNK 43|                    73|||||||94-UNK|||
                            24-UNK|||33-UNK 51                     86-UNK|||95-UNK||
                             25-UNK|| 38                            87-UNK|| 96-UNK|
                              26-UNK|                                88-UNK|  97-UNK
                               27-UNK                                 89-UNK   98-UNK
                                28-UNK                                 90-UNK   99-UNK
                                 29-UNK                                 91-UNK  100-UNK
                                  30-UNK                                 92-UNK  101-UNK
                                   31-UNK                                 93-UNK
   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  (0, 0)

(no "SCOP Domain" information available for 4M70)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M70)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M70)

(-) Gene Ontology  (2, 2)

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  Cis Peptide Bonds
    Ala K:85 - Val K:86   [ RasMol ]  
    Pro B:78 - Asp B:79   [ RasMol ]  
    Trp B:19 - Pro B:20   [ RasMol ]  
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