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 Diffractionresolution 3.10 Å
ligand MG, TPP enzyme
Primary referenceThermodynamic 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 (129 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.
  • 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_F] [3k0j_E] [3k0j_C] [3k0j_B] [3k0j_D] [3k0j]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 3K0J: [RRM ] by SMART
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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