3BO4 Nuclear Protein Rna date Dec 17, 2007
title A Relaxed Active Site Following Exon Ligation By A Group I Intron
authors S.V.Lipchock, S.A.Strobel
compound source
Molecule: U1 Small Nuclear Ribonucleoprotein A
Chain: A
Fragment: Rrm 1 Domain
Synonym: U1 Snrnp Protein A, U1a Protein, U1-A
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid

Molecule: Group I Intron P9
Chain: B
Engineered: Yes

Synthetic: Yes

Molecule: Dnarna (5'- R(Apapgpcpcpapcpapcpapapapcpcpa)-D(Pdg)- 3');
Chain: C
Engineered: Yes
Other_details: Ligated Exons

Synthetic: Yes

Molecule: Dnarna (5'-R(Cpa)-D(Pdu)- R(Papcpgpgpcpc)-3');
Chain: D
Engineered: Yes
Other_details: U1 Small Nuclear Ribonucleoprotein A Rna Binding Domain

Synthetic: Yes
symmetry Space Group: P 41 2 2
R_factor 0.280 R_Free 0.296
crystal
cell
length a length b length c angle alpha angle beta angle gamma
111.188 111.188 240.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.33 Å
ligand A23, GTP, K, MG enzyme
Primary referenceA relaxed active site after exon ligation by the group I intron., Lipchock SV, Strobel SA, Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5699-704. Epub 2008 Apr 11. PMID:18408159
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (116 Kb) [Save to disk]
  • Biological Unit Coordinates (3bo4.pdb1.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 3BO4
  • CSU: Contacts of Structural Units for 3BO4
  • Likely Quarternary Molecular Structure file(s) for 3BO4
  • Structure Factors (315 Kb)
  • Retrieve 3BO4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BO4 from S2C, [Save to disk]
  • Re-refined 3bo4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BO4 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 3BO4
  • 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 3BO4, from MSDmotif at EBI
  • Fold representative 3bo4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bo4_B] [3bo4_A] [3bo4_D] [3bo4] [3bo4_C]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 3BO4: [RRM ] by SMART
  • Other resources with information on 3BO4
  • Community annotation for 3BO4 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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