3UD4 Signaling Protein Rna date Oct 27, 2011
title The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
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(Gpa)-3')
Chain: B
Engineered: Yes
Other_details: Gpa

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.222 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.612 45.116 76.049 90.00 96.05 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand GTP, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
P


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] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (3ud4.pdb1.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 3UD4
  • CSU: Contacts of Structural Units for 3UD4
  • Structure Factors (139 Kb)
  • Retrieve 3UD4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3UD4 from S2C, [Save to disk]
  • Re-refined 3ud4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3UD4 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 3UD4
  • 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 3UD4, from MSDmotif at EBI
  • Fold representative 3ud4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ud4_R] [3ud4_B] [3ud4_P] [3ud4]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3UD4: [RRM ] by SMART
  • Other resources with information on 3UD4
  • Community annotation for 3UD4 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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