3E3J Transferase Rna Dna date Aug 07, 2008
title Crystal Structure Of An Intermediate Complex Of T7 Rnap And
authors K.J.Durniak, S.Bailey, T.A.Steitz
compound source
Molecule: Dna-Directed Rna Polymerase
Chain: C, B
Engineered: Yes
Mutation: Yes
Organism_scientific: Bacteriophage T7
Organism_taxid: 10760
Gene: 1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbh161

Molecule: Dna (28-Mer)
Chain: T, X
Engineered: Yes
Other_details: Template Dna

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Dtpdapdapdtpdapdcpdgpdapdcpdtpdcpdapdcpdtp Pdtpdtpdtpdcpdtpdgpdcpdcpdapdapdapdcpdgpdgpd
Chain: N, Y
Engineered: Yes
Other_details: Non-Template Dna

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Rna (5'-R(Gpgpgpapgpupapa)-3')
Chain: R, Z
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.392 R_Free 0.454
length a length b length c angle alpha angle beta angle gamma
99.216 180.602 198.619 90.00 90.00 90.00
method X-Ray Diffractionresolution 6.70 Å
enzyme Transferase E.C. BRENDA
C, B

Primary referenceThe structure of a transcribing t7 RNA polymerase in transition from initiation to elongation., Durniak KJ, Bailey S, Steitz TA, Science. 2008 Oct 24;322(5901):553-7. PMID:18948533
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (292 Kb) [Save to disk]
  • Biological Unit Coordinates (3e3j.pdb1.gz) 140 Kb
  • Biological Unit Coordinates (3e3j.pdb2.gz) 141 Kb
  • CSU: Contacts of Structural Units for 3E3J
  • Likely Quarternary Molecular Structure file(s) for 3E3J
  • Structure Factors (100 Kb)
  • Retrieve 3E3J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3E3J from S2C, [Save to disk]
  • Re-refined 3e3j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3E3J 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 3E3J
  • 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 3E3J, from MSDmotif at EBI
  • Fold representative 3e3j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3e3j] [3e3j_B] [3e3j_N] [3e3j_T] [3e3j_Y] [3e3j_R] [3e3j_X] [3e3j_C] [3e3j_Z]
  • SWISS-PROT database: [P00573]
  • Domain organization of [RPOL_BPT7] by SWISSPFAM
  • Domain found in 3E3J: [RPOL_N ] by SMART
  • Other resources with information on 3E3J
  • Community annotation for 3E3J 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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