3HJW Isomerase Rna date May 22, 2009
title Structure Of A Functional Ribonucleoprotein Pseudouridine Sy Bound To A Substrate Rna
authors B.Liang, J.Zhou, E.Kahen, R.M.Terns, M.P.Terns, H.Li
compound source
Molecule: Pseudouridine Synthase Cbf5
Chain: A
Synonym: Cbf5, Trna Pseudouridine 55 Synthase, Psi55 Syntha Uridine Isomerase, Trna Pseudouridylate Synthase;
Ec: 5.4.99.-
Engineered: Yes
Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261
Strain: Dsm 3638
Gene: Pf1785
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Codon Plus
Expression_system_vector_type: Plasmid

Molecule: Ribosome Biogenesis Protein Nop10
Chain: B
Engineered: Yes

Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261
Strain: Dsm 3638
Gene: Pf1141
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Codon Plus
Expression_system_vector_type: Plasmid

Molecule: 50s Ribosomal Protein L7ae
Chain: C
Engineered: Yes

Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261
Strain: Dsm 3638
Gene: Pf1367, Rpl7ae
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Codon Plus
Expression_system_vector_type: Plasmid

Molecule: Rna (58-Mer)
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: 5'-R(Gpapgpcpgp(Fhu)Pgpcpgpgpupupu)-
Chain: E
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.217 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
186.013 63.026 85.447 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand FHU, K, ZN enzyme Isomerase E.C.5.4.99 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C
  • ribonuclease P activity


  • Primary referenceStructure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA., Liang B, Zhou J, Kahen E, Terns RM, Terns MP, Li H, Nat Struct Mol Biol. 2009 May 28. PMID:19478803
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (3hjw.pdb1.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 3HJW
  • CSU: Contacts of Structural Units for 3HJW
  • Likely Quarternary Molecular Structure file(s) for 3HJW
  • Structure Factors (580 Kb)
  • Retrieve 3HJW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HJW from S2C, [Save to disk]
  • Re-refined 3hjw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HJW 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 3HJW
  • 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
  • 3D motif for 3HJW, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hjw] [3hjw_C] [3hjw_E] [3hjw_A] [3hjw_B] [3hjw_D]
  • SWISS-PROT database: [Q8U1R4] [Q8U160] [Q7LWY0]
  • Domain organization of [NOP10_PYRFU] [RL7A_PYRFU] [TRUB_PYRFU] by SWISSPFAM
  • Domains found in 3HJW: [DKCLD] [PUA ] by SMART
  • Other resources with information on 3HJW
  • Community annotation for 3HJW 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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