3OS0 Recombination Dna date Sep 08, 2010
title Pfv Strand Transfer Complex (Stc) At 2.81 A Resolution
authors G.N.Maertens, S.Hare, P.Cherepanov
compound source
Molecule: Integrase
Chain: A, B
Synonym: Pr125pol, Proteasereverse Transcriptaseribonucle P87pro-Rt-Rnaseh, Proteasereverse Transcriptase, P65pro-Rt Ribonuclease H, Rnase H, Integrase, In, P42in;
Engineered: Yes
 Organism_scientific: Human Spumaretrovirus
Organism_taxid: 11963
Strain: Pfv
Gene: Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Pc2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pssh6p-Pfv-Infl

Molecule: Dna (5'- D(Aptptpgptpcpaptpgpgpapaptptptpcpgpcpa)
Chain: C
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Oligonucleotide

Molecule: Dna (5'- D(Tpgpcpgpapapaptptpcpcpaptpgpapcpa)-3');
Chain: D
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Oligonucleotide

Molecule: Dna (5'-D(Cpcpcpgpapggpcpapcpgptpg)-
Chain: t
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Oligonucleotide

Molecule: Dna (5'- D(Pcptpapgpcpapcpgptpgpcpcptpcpgpgpg)-3');
Chain: T
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Oligonucleotide
symmetry Space Group: P 41 21 2
R_factor 0.208 R_Free 0.241
crystal
cell
length a length b length c angle alpha angle beta angle gamma
159.859 159.859 125.108 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.81 Å
ligand MG, ZN enzyme
note 3OS0 (Molecule of the Month:pdb135)
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThe mechanism of retroviral integration from X-ray structures of its key intermediates., Maertens GN, Hare S, Cherepanov P, Nature. 2010 Nov 11;468(7321):326-9. PMID:21068843
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (3os0.pdb1.gz) 216 Kb
  • LPC: Ligand-Protein Contacts for 3OS0
  • CSU: Contacts of Structural Units for 3OS0
  • Structure Factors (297 Kb)
  • Retrieve 3OS0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OS0 from S2C, [Save to disk]
  • Re-refined 3os0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3OS0 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 3OS0
  • 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 3OS0, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3os0] [3os0_t] [3os0_B] [3os0_A] [3os0_D] [3os0_C] [3os0_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3OS0
  • Community annotation for 3OS0 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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