3EGZ	Rna	date	Sep 11, 2008
title	Crystal Structure Of An In Vitro Evolved Tetracycline Aptame Artificial Riboswitch
authors	H.Xiao, T.E.Edwards, A.R.Ferre-D'Amare
compound		source
Molecule: U1 Small Nuclear Ribonucleoprotein A Chain: A Synonym: U1 Snrnp Protein A, U1a Protein, U1-A Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Snrpa Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet
Molecule: Tetracycline Aptamer And Artificial Riboswitch Chain: B Engineered: Yes		Synthetic: Yes Other_details: In Vitro Evolved Aptamer
symmetry	Space Group: P 4 21 2	R_factor 0.212 R_Free 0.260
crystal cell	length a length b length c angle alpha angle beta angle gamma 120.835 120.835 55.279 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	CTC, MG, MSE	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	Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch., Xiao H, Edwards TE, Ferre-D'Amare AR, Chem Biol. 2008 Oct 20;15(10):1125-37. PMID:18940672

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk] Biological Unit Coordinates (3egz.pdb1.gz) 184 Kb LPC: Ligand-Protein Contacts for 3EGZ CSU: Contacts of Structural Units for 3EGZ Likely Quarternary Molecular Structure file(s) for 3EGZ Structure Factors (317 Kb) Retrieve 3EGZ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3EGZ from S2C, [Save to disk] Re-refined 3egz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3EGZ 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 3EGZ

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3egz_A] [3egz_B] SWISS-PROT database: [P09012] Domain organization of [SNRPA_HUMAN] by SWISSPFAM Domain found in 3EGZ: [RRM ] by SMART Alignments of the sequence of 3EGZ with the sequences similar proteins can be viewed for 3EGZ'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 3EGZ

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

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