3HHN Ligase Rna date May 15, 2009
title Crystal Structure Of Class I Ligase Ribozyme Self-Ligation Product, In Complex With U1a Rbd
authors D.M.Shechner, R.A.Grant, S.C.Bagby, D.P.Bartel
compound source
Molecule: Class I Ligase Ribozyme, Self-Ligation Product
Chain: C, E
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Construct Transcribed In Vitro Using T7 Rna Polymerase Off Of A Linearized Plasmid Puc307hp;

Molecule: U1 Small Nuclear Ribonucleoprotein A
Chain: B, D
Fragment: Rna Binding Domain: Unp Residues 1-100
Synonym: U1 Snrnp Protein A, U1a Protein, 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: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Modified Pet11a
symmetry Space Group: P 1
R_factor 0.202 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.561 70.412 70.906 100.29 99.61 103.89
method X-Ray Diffractionresolution 2.99 Å
ligand A23, MG enzyme
Primary referenceCrystal structure of the catalytic core of an RNA-polymerase ribozyme., Shechner DM, Grant RA, Bagby SC, Koldobskaya Y, Piccirilli JA, Bartel DP, Science. 2009 Nov 27;326(5957):1271-5. PMID:19965478
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (163 Kb) [Save to disk]
  • Biological Unit Coordinates (3hhn.pdb1.gz) 154 Kb
  • LPC: Ligand-Protein Contacts for 3HHN
  • CSU: Contacts of Structural Units for 3HHN
  • Structure Factors (146 Kb)
  • Retrieve 3HHN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HHN from S2C, [Save to disk]
  • Re-refined 3hhn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HHN 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 3HHN
  • 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 3HHN, from MSDmotif at EBI
  • Fold representative 3hhn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hhn_D] [3hhn_B] [3hhn_E] [3hhn] [3hhn_C]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 3HHN: [RRM ] by SMART
  • Alignments of the sequence of 3HHN with the sequences similar proteins can be viewed for 3HHN's classification [SNRPA_HUMAN] 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 [SNRPA_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3HHN
  • Community annotation for 3HHN at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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