6PMI Transcription date Jul 02, 2019
title Sigm28-Transcription Initiation Complex With Specific Promot State 1
authors B.Liu, W.Shi
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 O157:H7
Organism_taxid: 83334
Gene: Rpoa, Z4665, Ecs4160
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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 O45:K1 (Strain S88
Organism_taxid: 585035
Strain: S88 Expec
Gene: Rpob, Ecs88_4448
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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 O157:H7
Organism_taxid: 83334
Gene: Rpoc, Z5561, Ecs4911
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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 O45:K1 (Strain S88
Organism_taxid: 585035
Strain: S88 Expec
Gene: Rpoz, Ecs88_4064
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna Polymerase Sigma Factor Flia
Chain: F
Synonym: Rna Polymerase Sigma Factor For Flagellar Operon,S Sigma-27,Sigma-28;
Engineered: Yes

Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Flia, Flad, Rpof, B1922, Jw1907
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Synthetic Nontemplate Strand Dna (54-Mer)
Chain: 1
Engineered: Yes

Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Synthetic Template Strand Dna (54-Mer)
Chain: 2
Engineered: Yes

Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Nascent Rna
Chain: 3
Engineered: Yes

Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
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 3.86 Å
ligand ATP, 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 referenceStructural basis of bacterial sigma(28) -mediated transcription reveals roles of the RNA polymerase zinc-binding domain., Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A, Hu Y, Liu B, EMBO J. 2020 Jun 2:e104389. doi: 10.15252/embj.2020104389. PMID:32484956
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (988 Kb) [Save to disk]
  • Biological Unit Coordinates (6pmi.pdb1.gz) 980 Kb
  • LPC: Ligand-Protein Contacts for 6PMI
  • CSU: Contacts of Structural Units for 6PMI
  • Retrieve 6PMI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6PMI from S2C, [Save to disk]
  • View 6PMI in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6PMI
  • Cartoon representation from PDB Cartoon
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  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6pmi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6pmi_A] [6pmi_1] [6pmi_3] [6pmi_C] [6pmi_F] [6pmi_D] [6pmi_E] [6pmi_B] [6pmi_2]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6PMI
  • Community annotation for 6PMI at PDBWiki (http://pdbwiki.org)

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