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(-) Description

Title :  CRYSTAL STRUCTURE OF RECOMBINANT FOOT-AND-MOUTH-DISEASE VIRUS A22-H2093F EMPTY CAPSID
 
Authors :  A. Kotecha, J. Seago, K. Scott, A. Burman, S. Loureiro, J. Ren, C. Porta, T. Jackson, E. Perez-Martin, C. A. Siebert, G. Paul, J. T. Huiskonen, I R. M. Esnouf, E. E. Fry, F. F. Maree, B. Charleston, D. I. Stuart
Date :  16 Aug 15  (Deposition) - 23 Sep 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (60x)
Keywords :  Foot And Mouth Disease Virus, Virus, Picornavirus, Vaccine, Aphthovirus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kotecha, J. Seago, K. Scott, A. Burman, S. Loureiro, J. Ren, C. Porta H. M. Ginn, T. Jackson, E. Perez-Martin, C. A. Siebert, G. Paul, J. T. Huiskonen, I. M. Jones, R. M. Esnouf, E. E. Fry, F. F. Maree, B. Charleston, D. I. Stuart
Structure-Based Energetics Of Protein Interfaces Guides Foot-And-Mouth Disease Virus Vaccine Design.
Nat. Struct. Mol. Biol. V. 22 788 2015
PubMed-ID: 26389739  |  Reference-DOI: 10.1038/NSMB.3096

(-) Compounds

Molecule 1 - VP1
    Chains: A
    Engineered: YES
    Expression System: MESOCRICETUS AURATUS
    Expression System Cell Line: BHK-21 CLONE 13
    Expression System Common: GOLDEN HAMSTER
    Expression System Taxid: 10036
    Organism Scientific: FOOT-AND-MOUTH DISEASE VIRUS - TYPE A
    Organism Taxid: 12111
    Strain: SEROTYPE A22 IRAQ
 
Molecule 2 - VP2
    Chains: B
    Engineered: YES
    Expression System: MESOCRICETUS AURATUS
    Expression System Cell Line: BHK-21, CLONE 13
    Expression System Common: GOLDEN HAMSTER
    Expression System Taxid: 10036
    Mutation: YES
    Organism Scientific: FOOT-AND-MOUTH DISEASE VIRUS - TYPE A
    Organism Taxid: 12111
    Strain: SEROTYPE A22 IRAQ
 
Molecule 3 - VP3
    Chains: C
    Engineered: YES
    Expression System: MESOCRICETUS AURATUS
    Expression System Cell Line: BHK-21, CLONE 13
    Expression System Common: GOLDEN HAMSTER
    Expression System Taxid: 10036
    Organism Scientific: FOOT-AND-MOUTH DISEASE VIRUS - TYPE A
    Organism Taxid: 12111
    Strain: SEROTYPE A22 IRAQ
 
Molecule 4 - VP4
    Chains: D
    Engineered: YES
    Expression System: MESOCRICETUS AURATUS
    Expression System Cell Line: BHK-21, CLONE 13
    Expression System Common: GOLDEN HAMSTER
    Expression System Taxid: 10036
    Organism Scientific: FOOT-AND-MOUTH DISEASE VIRUS - TYPE A
    Organism Taxid: 12111
    Strain: SEROTYPE A22 IRAQ

 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 5D8A)

(-) Sites  (0, 0)

(no "Site" information available for 5D8A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D8A)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:110 -Pro A:111
2Leu B:83 -Pro B:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D8A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D8A)

(-) Exons   (0, 0)

(no "Exon" information available for 5D8A)

(-) 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:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....hhhhhh.......hhhhhhhhhhh..ee......eee.hhhhh...hhhhhhhhheeeeeeeeeeeeeee..eeee....hhhhhhh....ee......eeeee........ee..................eee..eeeeeeeeeeeeeeeee....................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d8a A   1 TTTTGESADPVTTTVENYGGETQVQRRQHTDVTFIMDRFVKIQNLNPTHVIDLMQTHQHGLVGALLRAATYYFSDLEIVVRHDGNLTWVPNGAPEAALSNTGNPTAYLKAPFTRLALPYTAPHRVLATVYNGTSKAQLPASFNFGAIQATTIHELLVRMKRAELYCPRPLLAVEVSSQDRHKQKIIAPAK 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 160       170       180       190       200       210
                                                                                                                                                                135|                                                      
                                                                                                                                                                 156                                                      


Chain B from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..eeeee......ee..........hhhhh...ee.hhhh..eeeeeeee........eeeeee.....hhhhhhhhheeeeeeeeeeeeeee.....eeeeeeeeee.......hhhhhhhhh.eeee......eeeeee................eeeeeeeeeeee........eeeeeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d8a B  12 DRILTTRNGHTTSTTQSSVGVTYGYSTQEDHVSGPNTSGLETRVVQAERFFKKHLFDWTPDKAFGHLEKLELPTDHKGVYGFLVDSFAYMRNGWDVEVSAVGNQFNGGCLLVAMVPEWKEFTPREKYQLTLFPHQFISPRTNMTAHIVVPYLGVNRYDQYKKHKPWTLVVMVVSPLTTNTVSAGQIKVYANIAPTHVHVAGELPSKE 218
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       


Chain C from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................................hhhhhhhhh.ee........eee......eeeeeee....hhhhh.hhhhhhhh.eeeee..eeeeeee......eeeeeeeee.........hhhhhh..eeeeee.....eeeeee........ee.............eeeeeeeeee.....eeeeeeee....eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d8a C   1 GIVPVACSDGYGGLVTTDPKTADPVYGMVYNPPRTNYPGRFTNLLDVAEACPTFLCFDEGKPYVVTRTDEQRLLAKFDVSLAAKHMSNTYLSGIAQYYAQYSGTINLHFMFTGSTDSKARYMVAYVPPGVETPPDTPEKAAHCIHAEWDTGLNSKFTFSIPYVSAADYAYTASDVAETTNVQGWVCIYQITHGKAEQDTLVVSVSAGKDFELRLPIDPRSQ 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 


Chain D from PDB  Type:PROTEIN  Length:45
                                                                             
               SCOP domains --------------------------------------------- SCOP domains
               CATH domains --------------------------------------------- CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh.......hhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                 5d8a D  15 SGNTGSIINNYYMQQYQNSMDTQLNDWFSKLASSAFSGLFGALLA  85
                                    24        34   ||   70        80     
                                                  38|                    
                                                   65
   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 5D8A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D8A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D8A)

(-) Gene Ontology  (36, 36)

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  Cis Peptide Bonds
    Ala A:110 - Pro A:111   [ RasMol ]  
    Leu B:83 - Pro B:84   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/TrEMBL
        Q6PN23_9PICO | Q6PN23: 4gh4 4iv1 4iv3

(-) Related Entries Specified in the PDB File

4iv1 4IV1 CONTAINS THE WILDTYPE VIRAL CAPSID
4iv3 4IV3 CONTAINS THE SAME VIRAL CAPSID WITH VP2 S93C MUTATION.