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(-) Description

Title :  CRYSTAL STRUCTURE OF PARTITIVIRUS (PSV-F)
 
Authors :  J. Pan, L. Dong, L. Lin, W. F. Ochoa, R. S. Sinkovits, W. M. Havens, M. L. Nibert, T. S. Baker, S. A. Ghabrial, Y. J. Tao
Date :  03 Oct 08  (Deposition) - 10 Mar 09  (Release) - 31 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (60x)
Keywords :  Partitivirus, Rna Virus, Double Stranded Rna Virus, Dsrna Virus, T=2, "T=2" Capsid, Icosahedral Virus, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Pan, L. Dong, L. Lin, W. F. Ochoa, R. S. Sinkovits, W. M. Havens, M. L. Nibert, T. S. Baker, S. A. Ghabrial, Y. J. Tao
Atomic Structure Reveals The Unique Capsid Organization Of A Dsrna Virus.
Proc. Natl. Acad. Sci. Usa V. 106 4225 2009
PubMed-ID: 19246376  |  Reference-DOI: 10.1073/PNAS.0812071106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE CAPSID PROTEIN
    Chains: A, B
    Organism Scientific: PENICILLIUM STOLONIFERUM VIRUS F
    Organism Taxid: 296210
    Other Details: VIRUS PARTICLES WERE PRODUCED IN PENICILLIUM STOLONIFERUM ATCC 14586 (THE STRAIN NAME WAS NOT FOR THE VIRUS)
    Strain: ATCC 14586 (FOR THE HOST OF PSV-F)

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (60x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3ES5)

(-) Sites  (0, 0)

(no "Site" information available for 3ES5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ES5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:68 -Pro A:69
2Ile B:68 -Pro B:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ES5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ES5)

(-) Exons   (0, 0)

(no "Exon" information available for 3ES5)

(-) 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:379
 aligned with Q4G3H1_9VIRU | Q4G3H1 from UniProtKB/TrEMBL  Length:420

    Alignment length:379
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411         
         Q4G3H1_9VIRU    42 MRLGWIDPLPQVDTIFPLGLEPNVESIPAGEVELDFNLPETIAKPFADTVTSVGDRIQLVDDDKENIATSIYGLSFFKAARQLYSTMLDHEKAVNQPLKAVYYDETPIPAHMSGALGIIGHMKTKVGDVLVKDAGVLFKRGTAAGVTKFSEIDNDKTWNLDCSKLVWADHSSLSMIKRLASEKISQLVKQRYRVTDAQGHVYSVSMPQLTDQALPDYYDSIPDVAPNSDQLRVLTAALQMSLAQFRNDELPHDEDRSDLLTTLDLLYADGAYEISALRDQFELLMARYTTDFKWRVESIFKVGPPPAGTTGYGAQTVSSTGNTARWQFPLSDADINIGYLFSPSKSFSLFPKMVGYSKRAREDASASFANSDAKKFYAD 420
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................ee.....eeeee..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh...eehhhhhhhh....eee..eeeee.hhhhhhhhhhhhhhhhhh..........hhh.ee..hhhhhhhhhhhhhhhhhhhh...ee.........ee........hhhhhhhh......hhhhhhhhhhhh..hhhhhhh.......hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhheee..eeee....hhhhhhhhhhhh.eeeeee...eeee...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3es5 A  42 MRLGWIDPLPQVDTIFPLGLEPNVESIPAGEVELDFNLPETIAKPFADTVTSVGDRIQLVDDDKENIATSIYGLSFFKAARQLYSTMLDHEKAVNQPLKAVYYDETPIPAHMSGALGIIGHMKTKVGDVLVKDAGVLFKRGTAAGVTKFSEIDNDKTWNLDCSKLVWADHSSLSMIKRLASEKISQLVKQRYRVTDAQGHVYSVSMPQLTDQALPDYYDSIPDVAPNSDQLRVLTAALQMSLAQFRNDELPHDEDRSDLLTTLDLLYADGAYEISALRDQFELLMARYTTDFKWRVESIFKVGPPPAGTTGYGAQTVSSTGNTARWQFPLSDADINIGYLFSPSKSFSLFPKMVGYSKRAREDASASFANSDAKKFYAD 420
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411         


Chain B from PDB  Type:PROTEIN  Length:378
 aligned with Q4G3H1_9VIRU | Q4G3H1 from UniProtKB/TrEMBL  Length:420

    Alignment length:378
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411        
         Q4G3H1_9VIRU    42 MRLGWIDPLPQVDTIFPLGLEPNVESIPAGEVELDFNLPETIAKPFADTVTSVGDRIQLVDDDKENIATSIYGLSFFKAARQLYSTMLDHEKAVNQPLKAVYYDETPIPAHMSGALGIIGHMKTKVGDVLVKDAGVLFKRGTAAGVTKFSEIDNDKTWNLDCSKLVWADHSSLSMIKRLASEKISQLVKQRYRVTDAQGHVYSVSMPQLTDQALPDYYDSIPDVAPNSDQLRVLTAALQMSLAQFRNDELPHDEDRSDLLTTLDLLYADGAYEISALRDQFELLMARYTTDFKWRVESIFKVGPPPAGTTGYGAQTVSSTGNTARWQFPLSDADINIGYLFSPSKSFSLFPKMVGYSKRAREDASASFANSDAKKFYA 419
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......................ee.....eeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhh...eehhhhhhhh....eee..eeeee.hhhhhhhhhhhhhhhhhhhhhh..........ee..hhhhhhhhhhhhhhhhhhhh..ee...........ee.......hhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhheee..eeee....hhhhhhhhhhhh.eeeeee...eeee...hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3es5 B  42 MRLGWIDPLPQVDTIFPLGLEPNVESIPAGEVELDFNLPETIAKPFADTVTSVGDRIQLVDDDKENIATSIYGLSFFKAARQLYSTMLDHEKAVNQPLKAVYYDETPIPAHMSGALGIIGHMKTKVGDVLVKDAGVLFKRGTAAGVTKFSEIDNDKTWNLDCSKLVWADHSSLSMIKRLASEKISQLVKQRYRVTDAQGHVYSVSMPQLTDQALPDYYDSIPDVAPNSDQLRVLTAALQMSLAQFRNDELPHDEDRSDLLTTLDLLYADGAYEISALRDQFELLMARYTTDFKWRVESIFKVGPPPAGTTGYGAQTVSSTGNTARWQFPLSDADINIGYLFSPSKSFSLFPKMVGYSKRAREDASASFANSDAKKFYA 419
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411
   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  (0, 0)

(no "SCOP Domain" information available for 3ES5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ES5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ES5)

(-) Gene Ontology  (0, 0)

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  Cis Peptide Bonds
    Ile A:68 - Pro A:69   [ RasMol ]  
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1ej6 CRYSTAL STRUCTURE OF THE "T=2" INNER CORE OF MAMMALIAN ORTHOREOVIRUS
1k4r CRYSTAL STRUCTURE OF FLAVIVIRUS (DENGUE VIRUS), THE ASSEMBLY OF WHICH IS IN A MANNER SIMILAR TO PSV-F
1m1c CRYSTAL STRUCTURE OF THE "T=2" YEAST SACCHAROMYCES CEREVISIAE L-A VIRUS
1uf2 CRYSTAL STRUCTURE OF THE "T=2" INNER CORE OF PLANT REOVIRUS (RICE DWARF VIRUS)
2btv CRYSTAL STRUCTURE OF THE "T=2" INNER CORE OF BLUETONGUE ORBIVIRUS