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(-) Description

Title :  STRUCTURE OF ADENO-ASSOCIATED VIRUS SEROTYPE 8
 
Authors :  H. -J. Nam
Date :  14 Jun 07  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (60x)
Keywords :  Beta-Barrel, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Nam, M. D. Lane, E. Padron, B. Gurda, R. Mckenna, E. Kohlbrenner, G. Aslanidi, B. Byrne, N. Muzyczka, S. Zolotukhin, M. Agbandje-Mckenna
Structure Of Adeno-Associated Virus Serotype 8, A Gene Therapy Vector.
J. Virol. V. 81 12260 2007
PubMed-ID: 17728238  |  Reference-DOI: 10.1128/JVI.01304-07
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: VP1
    Organism Scientific: ADENO-ASSOCIATED VIRUS - 8
    Organism Taxid: 202813
    Strain: SEROTYPE 8

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (60x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:703 , SER A:705 , ASP A:714BINDING SITE FOR RESIDUE NA A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QA0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:521 -Pro A:522

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QA0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QA0)

(-) Exons   (0, 0)

(no "Exon" information available for 2QA0)

(-) 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:519
 aligned with Q8JQF8_9VIRU | Q8JQF8 from UniProtKB/TrEMBL  Length:738

    Alignment length:519
                                   229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729         
         Q8JQF8_9VIRU   220 DGVGSSSGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISNGTSGGATNDNTYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLSFKLFNIQVKEVTQNEGTKTIANNLTSTIQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFQFTYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLSRTQTTGGTANTQTLGFSQGGPNTMANQAKNWLPGPCYRQQRVSTTTGQNNNSNFAWTAGTKYHLNGRNSLANPGIAMATHKDDEERFFPSNGILIFGKQNAARDNADYSDVMLTSEEEIKTTNPVATEEYGIVADNLQQQNTAPQIGTVNSQGALPGMVWQNRDVYLQGPIWAKIPHTDGNFHPSPLMGGFGLKHPPPQILIKNTPVPADPPTTFNQSKLNSFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYYKSTSVDFAVNTEGVYSEPRPIGTRYLTRNL 738
               SCOP domains d2qa0a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2qa0A00 A:220-738 Empty Capsid Viral Protein 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains Parvo_coat-2qa0A01 A:220-716                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ---------------------- Pfam domains
         Sec.struct. author ............eeee...eeeeeeeeeeee..hhhhh.eeeee......hhhhheeeeeeeeeee...hhhhh.hhhhhhhhhhheeeeeeeeeeeeeeeeeeeeeeee..eeeeee.....eeeee.........................ee..eeeeee..............hhhhh..eee.....eeeeee..........ee................eeeeeee........eeeeeee.............ee..ee...eee.hhhhh...........eeee..eeee................eee.....eee.........hhh.eee..hhhhhhh........eeee...........eeee.ee.....ee............eee................eee......eeeee.....................eeeeeeeeeeeeeeeee...........................................ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qa0 A 220 DGVGSSSGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISNGTSGGATNDNTYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLSFKLFNIQVKEVTQNEGTKTIANNLTSTIQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFQFTYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLSRTQTTGGTANTQTLGFSQGGPNTMANQAKNWLPGPCYRQQRVSTTTGQNNNSNFAWTAGTKYHLNGRNSLANPGIAMATHKDDEERFFPSNGILIFGKQNAARDNADYSDVMLTSEEEIKTTNPVATEEYGIVADNLQQQNTAPQIGTVNSQGALPGMVWQNRDVYLQGPIWAKIPHTDGNFHPSPLMGGFGLKHPPPQILIKNTPVPADPPTTFNQSKLNSFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYYKSTSVDFAVNTEGVYSEPRPIGTRYLTRNL 738
                                   229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729
   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  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Parvo_coat] (8)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8JQF8_9VIRU | Q8JQF8)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.

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        Q8JQF8_9VIRU | Q8JQF8: 3ra2 3ra4 3ra8 3ra9 3raa

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