3BO3	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: Rna (5'- R(Apapgpcpcpapcpapcpapapapcpcpapg)-3'); Chain: C Engineered: Yes Other_details: 3' Exon		Synthetic: Yes
Molecule: Rna (5'-R(Cpapupapcpgpgpcpc)-3') Chain: D Engineered: Yes Other_details: U1 Small Nuclear Ribonucleoprotein A Rna Binding Domain, 5' Exon		Synthetic: Yes
symmetry	Space Group: P 41 2 2	R_factor 0.282 R_Free 0.325
crystal cell	length a length b length c angle alpha angle beta angle gamma 109.608 109.608 242.138 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.40 Å
ligand	A23, GTP, K, MG	enzyme
Gene Ontology	Chain Function Process Component A nucleotide binding nucleic acid binding RNA binding protein binding snRNA binding mRNA splicing, via spliceoso... mRNA processing RNA splicing gene expression nucleus nucleoplasm spliceosomal complex ribonucleoprotein complex
Primary reference	A 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 (3bo3.pdb1.gz) 111 Kb LPC: Ligand-Protein Contacts for 3BO3 CSU: Contacts of Structural Units for 3BO3 Likely Quarternary Molecular Structure file(s) for 3BO3 Structure Factors (264 Kb) Retrieve 3BO3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3BO3 from S2C, [Save to disk] Re-refined 3bo3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3BO3 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3BO3

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 3BO3, from MSDmotif at EBI Fold representative 3bo3 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3bo3_A] [3bo3_B] [3bo3_C] [3bo3_D] SWISS-PROT database: [P09012] Domain organization of [SNRPA_HUMAN] by SWISSPFAM Domain found in 3BO3: [RRM ] by SMART Alignments of the sequence of 3BO3 with the sequences similar proteins can be viewed for 3BO3's classification [SNRPA_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [SNRPA_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3BO3

Community annotation for 3BO3 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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