3IRW Rna Binding Protein Rna date Aug 24, 2009
title Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
authors K.D.Smith
compound source
Molecule: U1 Small Nuclear Ribonucleoprotein A
Chain: P
Fragment: Rna Binding 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
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11

Molecule: C-Di-Gmp Riboswitch
Chain: R
Engineered: Yes

Synthetic: Yes
Organism_scientific: Vibrio Cholerae
Organism_taxid: 666
Other_details: In Vitro Synthesis From A Plasmid Dna Templa Natural Sequence From Vibrio Cholerae
symmetry Space Group: P 1 21 1
R_factor 0.196 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.461 45.123 76.573 90.00 96.79 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand C2E, GTP, IRI, MG enzyme
note 3IRW (Molecule of the Month:pdb130)
Primary referenceStructural basis of ligand binding by a c-di-GMP riboswitch., Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA, Nat Struct Mol Biol. 2009 Dec;16(12):1218-23. Epub 2009 Nov 8. PMID:19898477
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (3irw.pdb1.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 3IRW
  • CSU: Contacts of Structural Units for 3IRW
  • Structure Factors (134 Kb)
  • Retrieve 3IRW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IRW from S2C, [Save to disk]
  • Re-refined 3irw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IRW 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 3IRW
  • 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 3IRW, from MSDmotif at EBI
  • Fold representative 3irw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3irw] [3irw_P] [3irw_R]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 3IRW: [RRM ] by SMART
  • Alignments of the sequence of 3IRW with the sequences similar proteins can be viewed for 3IRW'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 3IRW
  • Community annotation for 3IRW 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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