6GH5 Transcription date May 04, 2018
title Cryo-Em Structure Of Bacterial Rna Polymerase-Sigma54 Holoen Transcription Open Complex
authors R.Glyde, F.Z.Ye, X.D.Zhang
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
Engineered: Yes
 Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Gene: Rpoa, Pez, Phs, Sez, B3295, Jw3257
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
Expression_system_vector_type: Pgem

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
Engineered: Yes
Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Gene: Rpob, Gron, Nitb, Rif, Ron, Stl, Stv, Tabd, B3987, Jw
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
Expression_system_vector_type: Pgem

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
Engineered: Yes
Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Gene: Rpoc, Tabb, B3988, Jw3951
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
Expression_system_vector_type: Pgem

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
Engineered: Yes
Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Gene: Rpoz, B3649, Jw3624
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
Expression_system_vector_type: Pacycduet

Molecule: Rna Polymerase Sigma-54 Factor,Rna Polymerase Sig Factor,Rna Polymerase Sigma-54 Factor,Rna Polymerase Sigma- Rna Polymerase Sigma-54 Factor;
Chain: M
Ec: 2.7.7.6,2.7.7.6
Engineered: Yes
Mutation: Yes
Organism_scientific: Klebsiella Pneumoniae
Organism_taxid: 573
Gene: Sm87_03359
Expression_system: Escherichia Coli K-12
Expression_system_taxid: 83333
Expression_system_vector_type: Pet28b

Molecule: Nifh Promoter Template Dna
Chain: F
Engineered: Yes
Synthetic: Yes
Organism_scientific: Klebsiella Pneumoniae
Organism_taxid: 573

Molecule: Nifh Promoter Non-Template Dna
Chain: G
Engineered: Yes
Synthetic: Yes
Organism_scientific: Klebsiella Pneumoniae
Organism_taxid: 573
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.40 Å
ligand
enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


M
  • bacterial-type RNA polymeras...
  • bacterial sigma factor activ...


    • Primary referenceStructures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation., Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M, Zhang X, Mol Cell. 2018 Jun 21;70(6):1111-1120.e3. doi: 10.1016/j.molcel.2018.05.021. PMID:29932903
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (594 Kb) [Save to disk]
  • Biological Unit Coordinates (6gh5.pdb1.gz) 581 Kb
  • CSU: Contacts of Structural Units for 6GH5
  • Retrieve 6GH5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6GH5 from S2C, [Save to disk]
    • View 6GH5 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 6GH5
  • 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: [6gh5_D] [6gh5_G] [6gh5_B] [6gh5_C] [6gh5_E] [6gh5_F] [6gh5_M] [6gh5_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6GH5
  • Community annotation for 6GH5 at PDBWiki (http://pdbwiki.org)

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