3VAG Rna Binding Protein Dna date Dec 29, 2011
title Structure Of U2af65 Variant With Bru3c2 Dna
authors J.L.Jenkins, C.L.Kielkopf
compound source
Molecule: Splicing Factor U2af 65 Kda Subunit
Chain: A, B
Fragment: Rna Binding Domains 1 And 2
Synonym: U2 Auxiliary Factor 65 Kda Subunit, Hu2af(65), Hu2 Snrnp Auxiliary Factor Large Subunit;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: U2af2, U2af65
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p

Molecule: Dna 5'-D(Ucp(Bru)Pupupupu)-3'
Chain: P, E
Engineered: Yes
Other_details: Bru3c2 Dna

Synthetic: Yes
Other_details: Dna
symmetry Space Group: C 1 2 1
R_factor 0.191 R_Free 0.232
length a length b length c angle alpha angle beta angle gamma
166.825 37.499 100.925 90.00 125.35 90.00
method X-Ray Diffractionresolution 2.19 Å
ligand BRU, CPQ, DIO, GOL, SO4 enzyme
Primary referenceU2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs., Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf CL, Nucleic Acids Res. 2013 Feb 1. PMID:23376934
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (130 Kb) [Save to disk]
  • Biological Unit Coordinates (3vag.pdb1.gz) 124 Kb
  • LPC: Ligand-Protein Contacts for 3VAG
  • CSU: Contacts of Structural Units for 3VAG
  • Structure Factors (294 Kb)
  • Retrieve 3VAG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VAG from S2C, [Save to disk]
  • Re-refined 3vag structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VAG 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 3VAG
  • 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 3VAG, from MSDmotif at EBI
  • Fold representative 3vag from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vag] [3vag_A] [3vag_B] [3vag_E] [3vag_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3VAG: [RRM ] by SMART
  • Other resources with information on 3VAG
  • Community annotation for 3VAG at PDBWiki (http://pdbwiki.org)

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