3K0J	Rna Rna Binding Protein	date	Sep 24, 2009
title	Crystal Structure Of The E. Coli Thim Riboswitch In Complex With Thiamine Pyrophosphate And The U1a Crystallization Module
authors	N.Kulshina, T.E.Edwards, A.R.Ferre-D'Amare
compound		source
Molecule: U1 Small Nuclear Ribonucleoprotein A Chain: A, B, C, D Fragment: Unp Residues 2-97, Rrm 1 Domain Synonym: U1 Snrnp Protein A, U1a Protein, U1-A Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Snrpa, U1a Protein Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Rna (87-Mer) Chain: E, F Engineered: Yes		Synthetic: Yes
symmetry	Space Group: P 1 21 1	R_factor 0.197 R_Free 0.279
crystal cell	length a length b length c angle alpha angle beta angle gamma 52.250 71.600 128.350 90.00 94.62 90.00
method	X-Ray Diffraction	resolution	3.10 Å
ligand	MG, TPP	enzyme
Gene Ontology	Chain Function Process Component A, D, C, B 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	Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch., Kulshina N, Edwards TE, Ferre-D'Amare AR, RNA. 2010 Jan;16(1):186-96. Epub 2009 Nov 30. PMID:19948769

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (136 Kb) [Save to disk] Biological Unit Coordinates (3k0j.pdb1.gz) 67 Kb Biological Unit Coordinates (3k0j.pdb2.gz) 66 Kb LPC: Ligand-Protein Contacts for 3K0J CSU: Contacts of Structural Units for 3K0J Structure Factors (131 Kb) Retrieve 3K0J in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3K0J from S2C, [Save to disk] Re-refined 3k0j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3K0J 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 3K0J

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 3K0J, from MSDmotif at EBI Fold representative 3k0j from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3k0j_A] [3k0j_B] [3k0j_C] [3k0j_D] [3k0j_E] [3k0j_F] SWISS-PROT database: [P09012] Domain organization of [SNRPA_HUMAN] by SWISSPFAM Alignments of the sequence of 3K0J with the sequences similar proteins can be viewed for 3K0J'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 3K0J

Community annotation for 3K0J at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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