3RA4 Virus date Mar 27, 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

Molecule: Dna (5'-D(Cpa)-3')
Chain: D
Engineered: Yes

Organism_scientific: Aequorea Victoria
Organism_taxid: 6100
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 0.212 R_Free 0.213
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] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (3ra4.pdb1.gz) 5049 Kb
  • CSU: Contacts of Structural Units for 3RA4
  • Structure Factors (2127 Kb)
  • Retrieve 3RA4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RA4 from S2C, [Save to disk]
  • Re-refined 3ra4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RA4 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 3RA4
  • VIPERdb: visual, structural and computational analysis of 3RA4
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3RA4, from MSDmotif at EBI
  • Fold representative 3ra4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ra4_D] [3ra4_A] [3ra4]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3RA4
  • Community annotation for 3RA4 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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