6VVV Transcription,Transferase Dna date Feb 18, 2020
title Crystal Structure Of A Mycobacterium Smegmatis Transcription Initiation Complex With Rifampicin-Resistant Rna Polymerase
authors M.Lilic, S.A.Darst, E.A.Campbell
compound source
Molecule: Rna Polymerase-Binding Protein Rbpa
Chain: J
Engineered: Yes
 Organism_scientific: Mycolicibacterium Smegmatis (Strain At Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155
Gene: Rbpa, Msmeg_3858, Msmei_3768
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768

Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B, T
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Organism_scientific: Mycolicibacterium Smegmatis (Strain At Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

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: Mycolicibacterium Smegmatis (Strain At Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

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: Mycolicibacterium Smegmatis (Strain At Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

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: Mycolicibacterium Smegmatis (Strain At Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F
Organism_scientific: Mycolicibacterium Smegmatis (Strain At Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: Dna (31-Mer)
Chain: O
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (26-Mer)
Chain: P
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.234 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
129.748 162.344 137.155 90.00 111.27 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand SO4, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Primary referenceThe antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase., Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Muller R, Mooney R, Landick R, Darst SA, Campbell EA, Proc Natl Acad Sci U S A. 2020 Nov 16. pii: 2013706117. doi:, 10.1073/pnas.2013706117. PMID:33199626
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (476 Kb) [Save to disk]
  • Biological Unit Coordinates (6vvv.pdb1.gz) 463 Kb
  • LPC: Ligand-Protein Contacts for 6VVV
  • CSU: Contacts of Structural Units for 6VVV
  • Structure Factors (1792 Kb)
  • Retrieve 6VVV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6VVV from S2C, [Save to disk]
    • View 6VVV 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 6VVV
  • 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: [6vvv_T] [6vvv_J] [6vvv_O] [6vvv_E] [6vvv_F] [6vvv_D] [6vvv_A] [6vvv_P] [6vvv_C] [6vvv_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6VVV
  • Community annotation for 6VVV at PDBWiki (http://pdbwiki.org)

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