3UCU Signaling Protein Rna date Oct 27, 2011
title The C-Di-Gmp-I Riboswitch Bound To Pgpg
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: Diguanosine Monophosphate
Chain: A
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.215 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.088 45.350 77.243 90.00 96.24 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] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (3ucu.pdb1.gz) 55 Kb
  • LPC: Ligand-Protein Contacts for 3UCU
  • CSU: Contacts of Structural Units for 3UCU
  • Structure Factors (128 Kb)
  • Retrieve 3UCU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3UCU from S2C, [Save to disk]
  • Re-refined 3ucu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3UCU 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 3UCU
  • 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 3UCU, from MSDmotif at EBI
  • Fold representative 3ucu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ucu] [3ucu_P] [3ucu_A] [3ucu_R]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3UCU: [RRM ] by SMART
  • Alignments of the sequence of 3UCU with the sequences similar proteins can be viewed for 3UCU's classification 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 at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3UCU
  • Community annotation for 3UCU at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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