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(-) Description

Title :  STRUCTURAL STUDIES OF AAV8 CAPSID TRANSITIONS ASSOCIATED WITH ENDOSOMAL TRAFFICKING
 
Authors :  H. -J. Nam, B. Gurda, R. Mckenna, M. Porter, B. Byrne, M. Salganik, N. Muz M. Agbandje-Mckenna
Date :  27 Mar 11  (Deposition) - 21 Sep 11  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,D
Biol. Unit 1:  A,D  (60x)
Keywords :  Beta Barrel, Viral Capsid, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. J. Nam, B. L. Gurda, R. Mckenna, M. Potter, B. Byrne, M. Salganik, N. Muzyczka, M. Agbandje-Mckenna
Structural Studies Of Adeno-Associated Virus Serotype 8 Capsid Transitions Associated With Endosomal Trafficking.
J. Virol. V. 85 11791 2011
PubMed-ID: 21900159  |  Reference-DOI: 10.1128/JVI.05305-11

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineMAMMALIAN KIDNEY CELLS HEK293
    Expression System Taxid9606
    FragmentUNP RESIDUES 220-738
    Organism ScientificADENO-ASSOCIATED VIRUS - 8
    Organism Taxid202813
    StrainSEROTYPE 8
 
Molecule 2 - DNA (5'-D(P*CP*A)-3')
    ChainsD
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineMAMMALIAN KIDNEY CELLS HEK293
    Expression System Taxid9606
    Organism ScientificAEQUOREA VICTORIA
    Organism Taxid6100

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AD
Biological Unit 1 (60x)AD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3RA9)

(-) Sites  (0, 0)

(no "Site" information available for 3RA9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RA9)

(-) 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 3RA9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RA9)

(-) Exons   (0, 0)

(no "Exon" information available for 3RA9)

(-) 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 d3ra9a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee...eeeeeeeeeeee..hhhhh.eeeee......hhhhheeeeeeeeeee...hhhhh.hhhhhhhhhhheeeeeeeeeeeeeeeeeeeeeeee..eeeeee.....eeeee.........................ee..eeeeee..............hhhhh..eee.....eeeeee......ee.eee................eeeeeee........eeeeeee.hhhhh...........ee...eee.hhhhh...........eeee..eeee................eee.....eee.........hhh.eee..hhhhh..........eeee...........eeee.ee...................eee................eee......eeeee.....................eeeeeeeeeeeeeeeee..........................................eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ra9 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         

Chain D from PDB  Type:DNA  Length:2
                                  
                 3ra9 D   1 CA   2

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RA9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RA9)

(-) 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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  Cis Peptide Bonds
    Asn A:521 - Pro A:522   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/TrEMBL
        Q8JQF8_9VIRU | Q8JQF82qa0 3ra2 3ra4 3ra8 3raa

(-) Related Entries Specified in the PDB File

3ra2 3ra4 3ra8 3raa