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 3.12 Å
ligand A23, GTP, MG enzyme
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
  • Alignments of the sequence of 3R1L with the sequences similar proteins can be viewed for 3R1L'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 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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