5E18 Transcription Dna Rna date Sep 29, 2015
title T. Thermophilus Transcription Initiation Complex Having A Yy Discriminator Sequence And A Nontemplate-Strand Length Corr To Tss Selection At Position 8 (Rpo-Ccc-8)
authors Y.Zhang, R.H.Ebright
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C
Synonym: Rnap Subunit Beta,Rna Polymerase Subunit Beta,Tran Subunit Beta;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D
Synonym: Rnap Subunit Beta',Rna Polymerase Subunit Beta', Transcriptase Subunit Beta';
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Omega
Chain: E
Synonym: Rnap Omega Subunit,Rna Polymerase Omega Subunit, Transcriptase Subunit Omega;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F
Engineered: Yes
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579
Gene: Siga, Ttha0532
Expression_system: Escherichia Coli #1h766
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Dna (5'- D(Cpcptgpcpaptpcpcpgptpgpapgptpcpgpapgp
Chain: G
Engineered: Yes
Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Rna (5'-R(Cpcpcpupcpgpa)-3')
Chain: I
Engineered: Yes
Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Dna (28-Mer)
Chain: H
Engineered: Yes
Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: C 1 2 1
R_factor 0.238 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
185.917 103.241 298.404 90.00 97.93 90.00
method X-Ray Diffractionresolution 3.30 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


F
  • bacterial sigma factor activ...


    • Primary referenceMultiplexed protein-DNA cross-linking: Scrunching in transcription start site selection., Winkelman JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird JG, Taylor DM, Gourse RL, Ebright RH, Nickels BE, Science. 2016 Mar 4;351(6277):1090-3. doi: 10.1126/science.aad6881. PMID:26941320
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (583 Kb) [Save to disk]
  • Biological Unit Coordinates (5e18.pdb1.gz) 575 Kb
  • LPC: Ligand-Protein Contacts for 5E18
  • CSU: Contacts of Structural Units for 5E18
  • Structure Factors (770 Kb)
  • Retrieve 5E18 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5E18 from S2C, [Save to disk]
  • Re-refined 5e18 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5E18 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 5E18
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5e18_D] [5e18_E] [5e18_A] [5e18_F] [5e18] [5e18_C] [5e18_B] [5e18_H] [5e18_G] [5e18_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5E18: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
    • Other resources with information on 5E18
  • Community annotation for 5E18 at PDBWiki (http://pdbwiki.org)

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