3ER9 Transcription, Transferase Rna date Oct 01, 2008
title Crystal Structure Of The Heterodimeric Vaccinia Virus Mrna Polyadenylate Polymerase Complex With Uu And 3'-Deoxy Atp
authors C.Li, H.Li, S.Zhou, T.L.Poulos, P.D.Gershon
compound source
Molecule: Cap-Specific Mrna (Nucleoside-2'-O-)-Methyltransf
Chain: A
Synonym: Poly(A) Polymerase Regulatory Subunit, Poly(A) Pol Small Subunit, Pap-S, Vp39;
Ec: 2.1.1.57
Engineered: Yes
Mutation: Yes
Organism_scientific: Vaccinia Virus Wr
Organism_taxid: 10254
Strain: Western Reserve Wr
Gene: Paps, Vacwr095, F9
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plys
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Poly(A) Polymerase Catalytic Subunit
Chain: B
Synonym: Poly(A) Polymerase Large Subunit, Pap-L, Vp55
Ec: 2.7.7.19
Engineered: Yes
Mutation: Yes

Organism_scientific: Vaccinia Virus Wr
Organism_taxid: 10254
Strain: Western Reserve Wr
Gene: Papl, Vacwr057, E1l
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plys
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: 5'-R(Upu)-3'
Chain: D
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.208 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.531 91.977 133.734 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.06 Å
ligand 3AT, CA, GOL enzyme Transferase E.C.2.1.1.57 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referencePolymerase translocation with respect to single-stranded nucleic acid: looping or wrapping of primer around a poly(A) polymerase., Li C, Li H, Zhou S, Sun E, Yoshizawa J, Poulos TL, Gershon PD, Structure. 2009 May 13;17(5):680-9. PMID:19446524
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (133 Kb) [Save to disk]
  • Biological Unit Coordinates (3er9.pdb1.gz) 127 Kb
  • LPC: Ligand-Protein Contacts for 3ER9
  • CSU: Contacts of Structural Units for 3ER9
  • Likely Quarternary Molecular Structure file(s) for 3ER9
  • Structure Factors (409 Kb)
  • Retrieve 3ER9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ER9 from S2C, [Save to disk]
  • Re-refined 3er9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ER9 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 3ER9
  • 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 3ER9, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3er9_A] [3er9_B] [3er9_D] [3er9]
  • SWISS-PROT database: [P23371] [P07617]
  • Domain organization of [PAP1_VACCW] [PAP2_VACCW] by SWISSPFAM
  • Other resources with information on 3ER9
  • Community annotation for 3ER9 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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