5IPM Transcription, Transferase Dna Rna date Mar 09, 2016
title Sigmas-Transcription Initiation Complex With 4-Nt Nascent Rn
authors B.Liu, Y.Zuo, T.A.Steitz
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B
Fragment: Unp Residues 1-235
Synonym: Rnap Subunit Alpha, Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Rpoa, Pez, Phs, Sez, B3295, Jw3257
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C
Synonym: Rnap Subunit Beta, Rna Polymerase Subunit Beta, Transcriptase Subunit Beta;
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Rpob, Gron, Nitb, Rif, Ron, Stl, Stv, Tabd, B3987, Jw
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

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
Organism_taxid: 562
Gene: Rpoc, Tabb, B3988, Jw3951
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

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
Organism_taxid: 562
Gene: Rpoz, B3649, Jw3624
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Rna Polymerase Sigma Factor Rpos
Chain: F
Synonym: Sigma S, Sigma-38
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Rpos, Appr, Katf, Nur, Otsx, Sigs, B2741, Jw5437
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Synthetic Non-Template Strand Dna (50-Mer)
Chain: 1
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Synthetic Template Strand Dna (50-Mer)
Chain: 2
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Nascent Rna 4-Mer
Chain: 3
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.270 R_Free 0.330
crystal
cell
length a length b length c angle alpha angle beta angle gamma
132.752 151.967 228.064 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.20 Å
ligand GTP, 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 referenceStructures of E. coli sigmaS-transcription initiation complexes provide new insights into polymerase mechanism., Liu B, Zuo Y, Steitz TA, Proc Natl Acad Sci U S A. 2016 Mar 28. pii: 201520555. PMID:27035955
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1304 Kb) [Save to disk]
  • Biological Unit Coordinates (5ipm.pdb1.gz) 1292 Kb
  • LPC: Ligand-Protein Contacts for 5IPM
  • CSU: Contacts of Structural Units for 5IPM
  • Structure Factors (731 Kb)
  • Retrieve 5IPM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IPM from S2C, [Save to disk]
  • Re-refined 5ipm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5IPM 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 5IPM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5ipm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ipm_3] [5ipm_D] [5ipm_A] [5ipm_2] [5ipm_1] [5ipm_B] [5ipm_E] [5ipm_F] [5ipm_C] [5ipm]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5IPM: [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 5IPM
  • Community annotation for 5IPM at PDBWiki (http://pdbwiki.org)

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