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(-)Biological Unit 1
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(-) Description

Title :  REBUILD AND RE-REFINED MODEL FOR HUMAN PARECHOVIRUS 1
 
Authors :  S. Shakeel, E. C. Dykeman, S. J. White, A. Ora, J. J. B. Cockburn, S. J. But P. G. Stockley, R. Twarock
Date :  01 Dec 16  (Deposition) - 11 Jan 17  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.09
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (60x)
Keywords :  Virus, Parechovirus, Picornavirus, Rna, Human Parechovirus 1, Hpev1, Hpev (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Shakeel, E. C. Dykeman, S. J. White, A. Ora, J. J. Cockburn, S. J. Butcher, P. G. Stockley, R. Twarock
Genomic Rna Folding Mediates Assembly Of Human Parechovirus
Nat Commun V. 8 5 2017
PubMed-ID: 28232749  |  Reference-DOI: 10.1038/S41467-016-0011-Z

(-) Compounds

Molecule 1 - CAPSID SUBUNIT VP1
    Atcc: VR-52
    Chains: A
    EC Number: 3.6.1.15, 3.4.22.28, 2.7.7.48
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Atcc Number: CCL-185
    Expression System Cell Line: A549
    Expression System Common: HUMAN
    Expression System Organ: LUNG
    Expression System Taxid: 9606
    Expression System Tissue: LUNG CARCINOMA
    Organism Common: HPEV-1
    Organism Scientific: HUMAN PARECHOVIRUS 1 (STRAIN HARRIS)
    Organism Taxid: 103911
    Strain: HARRIS
 
Molecule 2 - CAPSID SUBUNIT VP3
    Atcc: VR-52
    Cell Line: A549
    Chains: B
    EC Number: 3.6.1.15, 3.4.22.28, 2.7.7.48
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Atcc Number: CCL-185
    Expression System Cell Line: A549
    Expression System Common: HUMAN
    Expression System Organ: LUNG
    Expression System Taxid: 9606
    Expression System Tissue: LUNG CARCINOMA
    Organism Common: HPEV-1
    Organism Scientific: HUMAN PARECHOVIRUS 1 (STRAIN HARRIS)
    Organism Taxid: 103911
    Strain: HARRIS
 
Molecule 3 - CAPSID SUBUNIT VP0
    Atcc: VR-52
    Chains: C
    EC Number: 3.6.1.15, 3.4.22.28, 2.7.7.48
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Atcc Number: CCL-185
    Expression System Cell Line: A549
    Expression System Common: HUMAN
    Expression System Organ: LUNG
    Expression System Taxid: 9606
    Expression System Tissue: LUNG CARCINOMA
    Organism Common: HPEV-1
    Organism Scientific: HUMAN PARECHOVIRUS 1 (STRAIN HARRIS)
    Organism Taxid: 103911
    Strain: HARRIS
 
Molecule 4 - RNA (5'-R(*GP*UP*UP*UP*UP*U)-3')
    Atcc: VR-52
    Chains: D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Atcc Number: CCL-185
    Expression System Cell Line: A549
    Expression System Common: HUMAN
    Expression System Organ: LUNG
    Expression System Taxid: 9606
    Expression System Tissue: LUNG CARCINOMA
    Organism Common: HPEV-1
    Organism Scientific: ECHOVIRUS 22 (STRAIN HARRIS)
    Organism Taxid: 103911

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (60x): ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5MJV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:40 -Pro A:41
2Gly C:33 -Asn C:34
3Leu C:141 -Pro C:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MJV)

(-) 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:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.eehhhhh...........................hhhhhh...eeeeeeee.....eeeee.....hhhhhhhhh.ee.eeeeeeeeee....eeeeeee....hhhhhhhhhhh.eeee...eeeeee........ee......eeeeeeee.......eeeeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5mjv A  25 TMSPNELGLTSAQDDGPLGQEKPNYFLNFRSMNVDIFTVSHTKVDNLFGRAWFFMEHTFTNEGQWRVPLEFPKQGHGSLSLLFAYFTGELNIHVLFLSERGFLRVAHTYDTSNDRVNFLSSNGVITVPAGEQMTLSAPYYSNKPLRTVRDNNSLGYLMCKPFLTGTSTGKIEVYLSLRCPNFFFPLPAPKVT 216
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214  


Chain B from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhh..ee...........hhhhh.......hhhhhh..ee.................eeeee.......eeeeeeehhhhhhhhhhhhh...eee..eeeeeeee.....eeeeeeeeee.............eeeeee.....eeeeee........ee......eeeeeeeeeeee.......eeeeeeeeee....ee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mjv B  15 MSTKYKWTRTKIDIAEGPGSMNMANVLCTTGAQSVALVGERAFYDPRTAGSKSRFDDLVKIAQLFSVMADSTTPSENHGVDAKGYFKWSATTAPQSIVHRNIVYLRLFPNLNVFVNSYSYFRGSLVLRLSVYASTFNRGRLRMGFFPNATTDSTSTLDNAIYTICDIGSDNSFEITIPYSFSTWMRKTNGHPIGLFQIEVLNRLTYNSSSPSEVYCIVQGKMGQDARFFCPTGSVVTFQ 253
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244         


Chain C from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh.....................eeeee..eeeee...........................hhhhhhhhh.eeeeeeee........eeeeeeehhhhhh.....hhhhhh...ee..eeeeeeee......eeeeeeeeehhhhhhh.......hhhhh.eeeee.....eeeeee........ee......eeeeeeeeeeee........eeeeeeeeeee................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mjv C  32 VGNEIGGNLLTKVADDASNILGPNCFATTAEPENKNVVQATTTVNTTNLTQHPSAPTMPFSPDFSNVDNFHSMAYDITTGDKNPSKLVRLETHEWTPSWARGYQITHVELPKVFWDHQDKPAYGQSRYFAAVRCGFHFQVQVNVNQGTAGSALVVYEPKPVVTYDSKLEFGAFTNLPHVLMNLAETTQADLCIPYVADTNYVKTDSSDLGQLKVYVWTPLSIPTGSANQVDVTILGSLLQLDFQNPRVFAQDVNIYD 288
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       


Chain D from PDB  Type:RNA  Length:6
                                      
                 5mjv D   1 GUUUUU   6
   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 5MJV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (42, 42)

Asymmetric Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 5mjv)
 
  Cis Peptide Bonds
    Gly A:40 - Pro A:41   [ RasMol ]  
    Gly C:33 - Asn C:34   [ RasMol ]  
    Leu C:141 - Pro C:142   [ RasMol ]  
 
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  2.7.7.48
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_HPE1H | Q66578: 4udf 4z92

(-) Related Entries Specified in the PDB File

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