3RA2 Virus date Mar 26, 2011
title Structural Studies Of Aav8 Capsid Transitions Associated Wit Endosomal Trafficking
authors H.J.Nam, B.Gurda, R.Mckenna, M.Porter, B.Byrne, M.Salganik, N.Muz M.Agbandje-Mckenna
compound source
Molecule: Capsid Protein
Chain: A
Fragment: Unp Residues 220-738
Engineered: Yes
 Organism_scientific: Adeno-Associated Virus - 8
Organism_taxid: 202813
Strain: Serotype 8
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Mammalian Kidney Cells Hek293
symmetry Space Group: P 63 2 2
R_factor 0.244 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
257.940 257.940 448.690 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural studies of AAV8 capsid transitions associated with endosomal trafficking., Nam HJ, Gurda BL, McKenna R, Potter M, Byrne B, Salganik M, Muzyczka N, Agbandje-McKenna M, J Virol. 2011 Sep 7. PMID:21900159
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (3ra2.pdb1.gz) 4922 Kb
  • CSU: Contacts of Structural Units for 3RA2
  • Structure Factors (1963 Kb)
  • Retrieve 3RA2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RA2 from S2C, [Save to disk]
  • Re-refined 3ra2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3RA2 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3RA2
  • VIPERdb: visual, structural and computational analysis of 3RA2
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3RA2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1i3ra2, region A:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d1k3ra2, region A:1-92,A:164-262 [Jmol] [rasmolscript] [script source]
        - Domain d1q3ra2, region A:217-369 [Jmol] [rasmolscript] [script source]
        - Domain d1b3ra2, region A:4-189,A:353-431 [Jmol] [rasmolscript] [script source]
        - Domain d1o3ra2, region A:8-137 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ra2] [3ra2_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3RA2
  • Community annotation for 3RA2 at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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