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(-) Description

Title :  CRYSTAL STRUCTURE OF 60-MER BFDV CAPSID PROTEIN IN COMPLEX WITH SINGLE STRANDED DNA
 
Authors :  S. Sarker, S. Raidal, D. Aragao, J. K. Forwood
Date :  30 Mar 16  (Deposition) - 04 May 16  (Release) - 12 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,B,C,D,E,F,G,H,I,J  (12x)
Keywords :  Bfdv Virus Capsid Jelly Roll, Viral Protein, Virus-Dna Complex (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: E, A, B, C, D
    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
 
Molecule 2 - SINGLE STRANDED DNA
    Chains: F, G, H, I, J
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFGHIJ
Biological Unit 1 (12x): ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1PO45Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 60)
No.NameCountTypeFull Name
1PO460Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY C:152 , LYS C:154 , ARG C:164 , SER E:43 , THR E:44binding site for residue PO4 E 301
2AC2SOFTWARESER A:43 , THR A:44 , LYS A:154 , ARG A:164 , HOH A:401 , HOH A:411binding site for residue PO4 A 301
3AC3SOFTWARESER B:43 , THR B:44 , LYS E:154 , ARG E:164binding site for residue PO4 B 301
4AC4SOFTWAREGLY B:152 , LYS B:154 , ARG B:164 , SER C:43 , THR C:44 , HOH C:415binding site for residue PO4 C 301
5AC5SOFTWARESER D:43 , THR D:44 , GLY D:152 , LYS D:154 , ARG D:164 , HOH D:401binding site for residue PO4 D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J37)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Tyr E:212 -Gly E:213
2Tyr A:212 -Gly A:213
3Tyr B:212 -Gly B:213
4Tyr C:212 -Gly C:213
5Tyr D:212 -Gly D:213

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J37)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J37)

(-) Exons   (0, 0)

(no "Exon" information available for 5J37)

(-) 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:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeeeee...........eeeeeeeehhhhhhh.........eeeeeeeeeeeeeeee..ee..ee..eeeeee..hhhhhhhh................eeee....eeeee..ee.eee.........eee...hhhhh.ee.......hhhhh.eeeeeeeee.....eeeeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j37 A  42 FSTNRIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPQITIEDLTTANQSAALWLNSARTGWIPLQGGPNSAGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFRQFAPNNPST 247
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      


Chain B from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeeeee...........eeeeeeeehhhhhhh.........eeeeeeeeeeeeeeee..ee..ee..eeeeee..hhhhhhhh................eeee....eeeee.....eee.........eee...hhhhh.ee.......hhhhh.eeeeeeeee.....eeeeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j37 B  42 FSTNRIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPQITIEDLTTANQSAALWLNSARTGWIPLQGGPNSAGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFRQFAPNNPST 247
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      


Chain C from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeeeee...........eeeeeeeehhhhhhh.........eeeeeeeeeeeeeeee......ee..eeeeee..hhhhhhhh................eeee....eeeee..ee.eee.........eee...hhhhh.ee.......hhhhh.eeeeeeeee.....eeeeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j37 C  42 FSTNRIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPQITIEDLTTANQSAALWLNSARTGWIPLQGGPNSAGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFRQFAPNNPST 247
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      


Chain D from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeeeee...........eeeeeeeehhhhhhh.........eeeeeeeeeeeeeeee..ee......eeeeee..hhhhhhhh................eeee....eeeee.....eee.........eee...hhhhh.ee.......hhhhh.eeeeeeeee.....eeeeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j37 D  42 FSTNRIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPQITIEDLTTANQSAALWLNSARTGWIPLQGGPNSAGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFRQFAPNNPST 247
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      


Chain E from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeeeee...........eeeeeeeehhhhhhh.........eeeeeeeeeeeeeee...ee..ee..eeeeee..hhhhhhhh................eeee....eeeee..ee.eee.........eee...hhhhh.ee.......hhhhh.eeeeeeeee.....eeeeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j37 E  42 FSTNRIYTLRLTRQFQFKINKQTTSVGNLIFNADYITFALDDFLQAVPNPHTLNFEDYRIKLAKMEMRPTGGHYTVQSDGFGHTAVIQDSRITRFKTTADQTQDPLAPFDGAKKWFVSRGFKRLLRPKPQITIEDLTTANQSAALWLNSARTGWIPLQGGPNSAGTKVRHYGIAFSFPQPEQTITYVTKLTLYVQFRQFAPNNPST 247
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      


Chain F from PDB  Type:DNA  Length:3
                                   
                 5j37 F 257 CGT 259


Chain G from PDB  Type:DNA  Length:3
                                   
                 5j37 G 257 CGT 259


Chain H from PDB  Type:DNA  Length:3
                                   
                 5j37 H 257 CGT 259


Chain I from PDB  Type:DNA  Length:3
                                   
                 5j37 I 257 CGT 259


Chain J from PDB  Type:DNA  Length:3
                                   
                 5j37 J 257 CGT 259
   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 5J37)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J37)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J37)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5J37)

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    Tyr A:212 - Gly A:213   [ RasMol ]  
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    Tyr D:212 - Gly D:213   [ RasMol ]  
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  5j37
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 Related Entries

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

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        A0A023R6W2_B | A0A023R6W2: 5j09 5j36

(-) Related Entries Specified in the PDB File

5j09 5j36