3R1L Rna Binding Protein Rna date Mar 10, 2011
title Crystal Structure Of The Class I Ligase Ribozyme-Substrate P Complex, C47u Mutant, Mg2+ Bound
authors D.M.Shechner, D.P.Bartel
compound source
Molecule: U1 Small Nuclear Ribonucleoprotein A
Chain: A, D
Fragment: Rna Binding Domain (Unp Residues 1-98)
Synonym: U1a, U1 Snrnp A, 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: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: P11u1adb

Molecule: 5'-R(Upcpcpapgpupa)-3'
Chain: B, E
Engineered: Yes
Other_details: Ligase Substrate

Synthetic: Yes

Molecule: Class I Ligase Ribozyme
Chain: C, F
Engineered: Yes
Mutation: Yes
Other_details: Unligated C47u Mutant

Synthetic: Yes
Other_details: Rna Was Prepared By In Vitro Transcription W Rna Polymerase From Linearized Plasmid P307hu_c47u
symmetry Space Group: P 1
R_factor 0.197 R_Free 0.240
length a length b length c angle alpha angle beta angle gamma
59.190 70.237 71.214 99.86 99.34 103.81
method X-Ray Diffractionresolution 3.13 Å
ligand A23, GTP, MG enzyme
A, D

Primary referenceThe structural basis of RNA-catalyzed RNA polymerization., Shechner DM, Bartel DP, Nat Struct Mol Biol. 2011 Aug 21;18(9):1036-42. doi: 10.1038/nsmb.2107. PMID:21857665
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (159 Kb) [Save to disk]
  • Biological Unit Coordinates (3r1l.pdb1.gz) 76 Kb
  • Biological Unit Coordinates (3r1l.pdb2.gz) 76 Kb
  • LPC: Ligand-Protein Contacts for 3R1L
  • CSU: Contacts of Structural Units for 3R1L
  • Structure Factors (138 Kb)
  • Retrieve 3R1L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3R1L from S2C, [Save to disk]
  • Re-refined 3r1l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3R1L 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 3R1L
  • 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 3R1L, from MSDmotif at EBI
  • Fold representative 3r1l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3r1l_F] [3r1l_E] [3r1l_A] [3r1l_B] [3r1l_C] [3r1l_D] [3r1l]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3R1L: [RRM ] by SMART
  • Other resources with information on 3R1L
  • Community annotation for 3R1L at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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