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(-) Description

Title :  CRYSTAL STRUCTURE OF DECAMERIC BFDV CAPSID PROTEIN
 
Authors :  S. Sarker, S. Raidal, D. Aragao, J. K. Forwood
Date :  28 Mar 16  (Deposition) - 04 May 16  (Release) - 12 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Bfdv Virus Capsid Jelly Roll, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sarker, M. C. Terron, Y. Khandokar, D. Aragao, J. M. Hardy, M. Radjainia, M. Jimenez-Zaragoza, P. J. De Pablo, F. Coulibaly, D. Luque, S. R. Raidal, J. K. Forwood
Structural Insights Into The Assembly And Regulation Of Distinct Viral Capsid Complexes.
Nat Commun V. 7 13014 2016
PubMed-ID: 27698405  |  Reference-DOI: 10.1038/NCOMMS13014

(-) Compounds

Molecule 1 - BEAK AND FEATHER DISEASE VIRUS CAPSID PROTEIN
    Chains: A, B, C, D, E, F, G, H, I, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CAP
    Organism Common: BFDV
    Organism Scientific: BEAK AND FEATHER DISEASE VIRUS
    Organism Taxid: 77856

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5J09)

(-) Sites  (0, 0)

(no "Site" information available for 5J09)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J09)

(-) Cis Peptide Bonds  (13, 13)

Asymmetric/Biological Unit
No.Residues
1Tyr A:212 -Gly A:213
2Tyr B:212 -Gly B:213
3Tyr C:212 -Gly C:213
4Tyr D:212 -Gly D:213
5Lys E:137 -Thr E:138
6Tyr E:212 -Gly E:213
7Val F:88 -Pro F:89
8Tyr F:212 -Gly F:213
9Tyr G:212 -Gly G:213
10Val H:88 -Pro H:89
11Tyr H:212 -Gly H:213
12Tyr I:212 -Gly I:213
13Tyr J:212 -Gly J:213

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J09)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J09)

(-) Exons   (0, 0)

(no "Exon" information available for 5J09)

(-) Sequences/Alignments

Asymmetric/Biological 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:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee...........eeeeeeeehhhhhh............eeeeeeeeeeeeee..........eeeeee..hhhhhhhh................eeee....eeeee.....hhhhh.ee...hhhhh.eeeeeeeee.....eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j09 A  46 RIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPNSARTGWIPLQSAGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFR 238
                                    55        65        75        85        95       105       115       125       135       145       155       165    || 193     ||207       217       227       237 
                                                                                                                                                      170|       199|                                  
                                                                                                                                                       189        204                                  


Chain B from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...........eeeeeeeehhhhhh....hhhhh...eeeeeeeeeeeeee..........eeeeee..hhhhhhhh................eeee....eeeee.....hhhhh.ee......eeeeeeeee.....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j09 B  46 RIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPNSARTGWIPLGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFRQ 239
                                    55        65        75        85        95       105       115       125       135       145       155       165    || 193    || 210       220       230         
                                                                                                                                                      170|      198|                                 
                                                                                                                                                       189       206                                 


Chain C from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee...........eeeeeeeehhhhh.....hhhhh...eeeeeeeeeeeeee..........eeeeee..hhhhhhhh................eeee....eeeee.....hhhhh.ee......eeeeeeeee.....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j09 C  46 RIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPNSARTGWIPLGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFRQ 239
                                    55        65        75        85        95       105       115       125       135       145       155       165    || 193    || 210       220       230         
                                                                                                                                                      170|      198|                                 
                                                                                                                                                       189       206                                 


Chain D from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...........eeeeeeeehhhhhh....hhhhh...eeeeeeeeeeeee...........eeeeee..hhhhhhhh................eeee....eeeee.....hhhhh.ee..hhhhh.eeeeeeeee.....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j09 D  46 RIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPNSARTGWIPLQAGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFRQ 239
                                    55        65        75        85        95       105       115       125       135       145       155       165    || 193     ||208       218       228       238 
                                                                                                                                                      170|       199|                                  
                                                                                                                                                       189        205                                  


Chain E from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...........eeeeeeeehhhhhh....hhhhh...eeeeeeeeeeeeee..........eeeeee..hhhhhhh.................eeee....eeeee.....hhhhh.ee.hhhhh.eeeeeeeee.....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j09 E  46 RIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPNSARTGWIPLAGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFRQ 239
                                    55        65        75        85        95       105       115       125       135       145       155       165    || 193    || 209       219       229       239
                                                                                                                                                      170|      198|                                  
                                                                                                                                                       189       205                                  


Chain F from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee...........eeeeeeeehhhhhh....hhhhh...eeeeeeeeeeeee...........eeeeee..hhhhhhhh................eeee....eeeee.....hhhhh.ee.hhhhh.eeeeeeeee.....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j09 F  46 RIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPNSARTGWIPLAGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFRQ 239
                                    55        65        75        85        95       105       115       125       135       145       155       165    || 193    || 209       219       229       239
                                                                                                                                                      170|      198|                                  
                                                                                                                                                       189       205                                  


Chain G from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...........eeeeeeeehhhhhh....hhhhh...eeeeeeeeeeeeee..........eeeeee..hhhhhhhh................eeee....eeeee.....hhhhh.ee.hhhhh.eeeeeeeee.....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j09 G  46 RIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPNSARTGWIPLAGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFRQ 239
                                    55        65        75        85        95       105       115       125       135       145       155       165    || 193    || 209       219       229       239
                                                                                                                                                      170|      198|                                  
                                                                                                                                                       189       205                                  


Chain H from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee...........eeeeeeeehhhhhh....hhhhh...eeeeeeeeeeeeee..........eeeeee..hhhhhhhh................eeee....eeeee.....hhhhh.ee......eeeeeeeee.....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j09 H  46 RIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPNSARTGWIPLGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFRQ 239
                                    55        65        75        85        95       105       115       125       135       145       155       165    || 193    || 210       220       230         
                                                                                                                                                      170|      198|                                 
                                                                                                                                                       189       206                                 


Chain I from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...........eeeeeeeehhhhhh....hhhhh...eeeeeeeeeeeeee..........eeeeee..hhhhhhhh................eeee....eeeee.....hhhhh.ee......eeeeeeeee.....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j09 I  46 RIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPNSARTGWIPLGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFRQ 239
                                    55        65        75        85        95       105       115       125       135       145       155       165    || 193    || 210       220       230         
                                                                                                                                                      170|      198|                                 
                                                                                                                                                       189       206                                 


Chain J from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...........eeeeeeeehhhhhh....hhhhh...eeeeeeeeeeeeee..........eeeeee..hhhhhhhh................eeee....eeeee.....hhhhh.ee.hhhhh.eeeeeeeee.....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j09 J  46 RIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPNSARTGWIPLAGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFRQ 239
                                    55        65        75        85        95       105       115       125       135       145       155       165    || 193    || 209       219       229       239
                                                                                                                                                      170|      198|                                  
                                                                                                                                                       189       205
   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 5J09)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J09)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J09)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5J09)

 Visualization

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5j09)
 
  Sites
(no "Sites" information available for 5j09)
 
  Cis Peptide Bonds
    Lys E:137 - Thr E:138   [ RasMol ]  
    Tyr A:212 - Gly A:213   [ RasMol ]  
    Tyr B:212 - Gly B:213   [ RasMol ]  
    Tyr C:212 - Gly C:213   [ RasMol ]  
    Tyr D:212 - Gly D:213   [ RasMol ]  
    Tyr E:212 - Gly E:213   [ RasMol ]  
    Tyr F:212 - Gly F:213   [ RasMol ]  
    Tyr G:212 - Gly G:213   [ RasMol ]  
    Tyr H:212 - Gly H:213   [ RasMol ]  
    Tyr I:212 - Gly I:213   [ RasMol ]  
    Tyr J:212 - Gly J:213   [ RasMol ]  
    Val F:88 - Pro F:89   [ RasMol ]  
    Val H:88 - Pro H:89   [ RasMol ]  
 

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  5j09
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  A0A023R6W2_B | A0A023R6W2
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A0A023R6W2_B | A0A023R6W2: 5j36 5j37

(-) Related Entries Specified in the PDB File

5j36 5j37