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(-) Description

Title :  STRUCTURAL CHARACTERIZATION OF THE DUAL GLYCAN BINDING ADENO-ASSOCIATED VIRUS SEROTYPE 6
 
Authors :  R. Ng, M. Agbandje-Mckenna
Date :  05 Aug 10  (Deposition) - 23 Mar 11  (Release) - 19 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (60x)
Keywords :  Beta-Barrel, Ssdna Binding, Ssdna, Icosahedral Virus, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Ng, L. Govindasamy, B. L. Gurda, R. Mckenna, O. G. Kozyreva, R. J. Samulski, K. N. Parent, T. S. Baker, M. Agbandje-Mckenna
Structural Characterization Of The Dual Glycan Binding Adeno-Associated Virus Serotype 6.
J. Virol. V. 84 12945 2010
PubMed-ID: 20861247  |  Reference-DOI: 10.1128/JVI.01235-10

(-) Compounds

Molecule 1 - CAPSID PROTEIN VP1
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Organism Scientific: ADENO-ASSOCIATED VIRUS - 6
    Organism Taxid: 68558

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CYT1Ligand/Ion6-AMINOPYRIMIDIN-2(1H)-ONE
2OAH1Ligand/Ion9-(2-DEOXY-5-O-PHOSPHONO-ALPHA-D-THREO-PENTOFURANOSYL)-9H-PURIN-6-AMINE
Biological Unit 1 (2, 120)
No.NameCountTypeFull Name
1CYT60Ligand/Ion6-AMINOPYRIMIDIN-2(1H)-ONE
2OAH60Ligand/Ion9-(2-DEOXY-5-O-PHOSPHONO-ALPHA-D-THREO-PENTOFURANOSYL)-9H-PURIN-6-AMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:627 , HIS A:628 , PHE A:629BINDING SITE FOR RESIDUE CYT A 737
2AC2SOFTWAREGLU A:417 , VAL A:419 , ASP A:609 , HIS A:628 , HIS A:630 , SER A:632 , GLY A:639 , LYS A:641BINDING SITE FOR RESIDUE OAH A 999

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:218 -Asp A:219
2Asn A:519 -Pro A:520

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OAH)

(-) 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 O56137_9VIRU | O56137 from UniProtKB/TrEMBL  Length:736

    Alignment length:519
                                   227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727         
         O56137_9VIRU   218 ADGVGNASGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANNLTSTVQVFSDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLNRTQNQSGSAQNKDLLFSRGSPAGMSVQPKNWLPGPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHKDDKDKFFPMSGVMIFGKESAGASNTALDNVMITDEEEIKATNPVATERFGTVAVNLQSSSTDPATGDVHVMGALPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPPAEFSATKFASFITQYSTGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGLYTEPRPIGTRYLTRPL 736
               SCOP domains d3oaha_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Parvo_coat-3oahA01 A:218-714                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ---------------------- Pfam domains
         Sec.struct. author .............eeee...eeeeeeeeeeee........eeee............eeeeeeeeee...hhhhh.hhhhhhhhhhheeeeeeeeeeeeeeeeeeeeeeee..eeeeee.....eeeee........................eee..eeeeee.ee..ee.......hhhhh..eee.....eeeeee......ee.eee................eeeeeeee......eeeeeeee.hhhhhhhh........ee...eee.hhhhh...hhhhhh..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
                 3oah A 218 ADGVGNASGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANNLTSTVQVFSDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLNRTQNQSGSAQNKDLLFSRGSPAGMSVQPKNWLPGPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHKDDKDKFFPMSGVMIFGKESAGASNTALDNVMITDEEEIKATNPVATERFGTVAVNLQSSSTDPATGDVHVMGALPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPPAEFSATKFASFITQYSTGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGLYTEPRPIGTRYLTRPL 736
                                   227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727
   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  (0, 0)

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

(-) 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   (O56137_9VIRU | O56137)
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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  3oah
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  O56137_9VIRU | O56137
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 Related Entries

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

UniProtKB/TrEMBL
        O56137_9VIRU | O56137: 3shm 4v86

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3OAH)