6CCV Transcription date Feb 07, 2018
title Crystal Structure Of A Mycobacterium Smegmatis Rna Polymeras Transcription Initiation Complex With Inhibitor Rifampicin
authors M.Lilic, S.A.Darst, E.A.Campbell
compound source
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: Mycobacterium Smegmatis (Strain Atcc 7 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: Mycobacterium Smegmatis (Strain Atcc 7 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: Mycobacterium Smegmatis (Strain Atcc 7 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: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F
Engineered: Yes

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155
Gene: Siga, Msmeg_2758
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Unknown Peptide
Chain: G
Engineered: Yes

Organism_scientific: Mycobacterium Smegmatis Str. Mc2 155
Organism_taxid: 246196
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna Polymerase-Binding Protein Rbpa
Chain: J
Engineered: Yes

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155
Gene: Rbpa, Msmeg_3858, Msmei_3768
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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 0.223 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
132.353 162.325 139.401 90.00 107.37 90.00
method X-Ray Diffractionresolution 3.05 Å
ligand EDO, GLU, RFP, SO4, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, T, B


C


D


E


F
  • bacterial sigma factor activ...


  • J


    Primary referenceRifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism., Peek J, Lilic M, Montiel D, Milshteyn A, Woodworth I, Biggins JB, Ternei MA, Calle PY, Danziger M, Warrier T, Saito K, Braffman N, Fay A, Glickman MS, Darst SA, Campbell EA, Brady SF, Nat Commun. 2018 Oct 8;9(1):4147. doi: 10.1038/s41467-018-06587-2. PMID:30297823
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (561 Kb) [Save to disk]
  • Biological Unit Coordinates (6ccv.pdb1.gz) 546 Kb
  • LPC: Ligand-Protein Contacts for 6CCV
  • CSU: Contacts of Structural Units for 6CCV
  • Structure Factors (2354 Kb)
  • Retrieve 6CCV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6CCV from S2C, [Save to disk]
  • View 6CCV 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 6CCV
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6ccv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ccv_D] [6ccv_P] [6ccv_E] [6ccv_T] [6ccv_O] [6ccv_B] [6ccv_F] [6ccv_G] [6ccv_A] [6ccv_C] [6ccv_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6CCV
  • Community annotation for 6CCV at PDBWiki (http://pdbwiki.org)

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