3VAL Rna Binding Protein Dna date Dec 29, 2011
title Structure Of U2af65 Variant With Bru5c1 Dna
authors J.L.Jenkins, K.H.Frato, C.L.Kielkopf
compound source
Molecule: Splicing Factor U2af 65 Kda Subunit
Chain: A, B, D, I
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(Cupupup(Bru)Pupu)-3')
Chain: E, H, K, P
Engineered: Yes

Synthetic: Yes
Other_details: Dna
symmetry Space Group: P 1 21 1
R_factor 0.208 R_Free 0.271
length a length b length c angle alpha angle beta angle gamma
37.583 137.081 83.962 90.00 102.97 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand BRU, DIO, 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 (3val.pdb1.gz) 124 Kb
  • LPC: Ligand-Protein Contacts for 3VAL
  • CSU: Contacts of Structural Units for 3VAL
  • Structure Factors (572 Kb)
  • Retrieve 3VAL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VAL from S2C, [Save to disk]
  • Re-refined 3val structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VAL 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 3VAL
  • 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 3VAL, from MSDmotif at EBI
  • Fold representative 3val from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3val_D] [3val_I] [3val_B] [3val_H] [3val] [3val_E] [3val_K] [3val_P] [3val_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3VAL: [RRM ] by SMART
  • Other resources with information on 3VAL
  • Community annotation for 3VAL at PDBWiki (http://pdbwiki.org)

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