3UCZ Signaling Protein Rna date Oct 27, 2011
title The C-Di-Gmp-I Riboswitch Bound To Gpg
authors K.D.Smith, S.A.Strobel
compound source
Molecule: U1 Small Nuclear Ribonucleoprotein A
Chain: P
Fragment: Rna Binding Domain, Unp Residues 1-98
Synonym: U1 Snrnp A, U1-A, U1a
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: Rna (92-Mer)
Chain: R
Engineered: Yes
Other_details: C-Di-Gmp-I Riboswitch

Synthetic: Yes
Other_details: In Vitro Transcribed Rna Transcript

Molecule: Rna (5'-R(Gpg)-3')
Chain: D
Engineered: Yes
Other_details: Gpg

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.202 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.808 45.358 77.334 90.00 95.81 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand GTP, MG enzyme
Primary referenceStructural and biochemical characterization of linear dinucleotide analogs bound to the c-di-GMP-I aptamer., Smith KD, Lipchock SV, Strobel SA, Biochemistry. 2011 Dec 8. PMID:22148472
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (3ucz.pdb1.gz) 113 Kb
  • LPC: Ligand-Protein Contacts for 3UCZ
  • CSU: Contacts of Structural Units for 3UCZ
  • Structure Factors (128 Kb)
  • Retrieve 3UCZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3UCZ from S2C, [Save to disk]
  • Re-refined 3ucz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3UCZ 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 3UCZ
  • 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 3UCZ, from MSDmotif at EBI
  • Fold representative 3ucz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ucz_R] [3ucz_D] [3ucz_P] [3ucz]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3UCZ: [RRM ] by SMART
  • Other resources with information on 3UCZ
  • Community annotation for 3UCZ at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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