6TYE

Crystal structure of MTB sigma L transcription initiation complex with 5 nt long RNA primer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.79 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.

Li, L.Molodtsov, V.Lin, W.Ebright, R.H.Zhang, Y.

(2020) Proc.Natl.Acad.Sci.USA 117: 5801-5809

  • DOI: 10.1073/pnas.1920747117
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in ...

    All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the "σ-finger" of the bacterial transcription initiation factor σ. The structures reveal that-for both the primary σ-factor and extracytoplasmic (ECF) σ-factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA-the "σ-finger" is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from ∼5 nt to ∼10 nt.


    Related Citations: 
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution.
      Adams, P.D.,Afonine, P.V.,Bunkoczi, G.,Chen, V.B.,Davis, I.W.,Echols, N.,Headd, J.J.,Hung, L.W.,Kapral, G.J.,Grosse-Kunstleve, R.W.,McCoy, A.J.,Moriarty, N.W.,Oeffner, R.,Read, R.J.,Richardson, D.C.,Richardson, J.S.,Terwilliger, T.C.,Zwart, P.H.
      (2010) Acta Crystallogr.,Sect.D 66: 213
    • Towards automated crystallographic structure refinement with phenix.refine.
      Afonine, P.V.,Grosse-Kunstleve, R.W.,Echols, N.,Headd, J.J.,Moriarty, N.W.,Mustyakimov, M.,Terwilliger, T.C.,Urzhumtsev, A.,Zwart, P.H.,Adams, P.D.
      (2012) Acta Crystallogr.,Sect.D 68: 352


    Organizational Affiliation

    Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854; ebright@waksman.rutgers.edu yzhang@sippe.ac.cn.,Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854.,Department of Chemistry, Rutgers University, Piscataway, NJ 08854.,Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032 Shanghai, China; ebright@waksman.rutgers.edu yzhang@sippe.ac.cn.,Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032 Shanghai, China.,University of Chinese Academy of Sciences, 100049 Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor
F
177Mycobacterium tuberculosisMutation(s): 0 
Gene Names: sigX (sigL)
Find proteins for A0A045IR27 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045IR27
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B
347Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)Mutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for A5U8D3 (Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra))
Go to UniProtKB:  A5U8D3
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C
1178Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for P9WGY8 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Go to UniProtKB:  P9WGY8
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1316N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E
110Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for A0A045H2R3 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045H2R3
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*AP*TP*CP*GP*AP*GP*G)-3')G17Mycobacterium tuberculosis
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*TP*GP*TP*CP*AP*GP*TP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*C)-3')H27Mycobacterium tuberculosis
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(P*CP*UP*CP*GP*A)-3')I5Mycobacterium tuberculosis
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.79 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 129.527α = 90.00
b = 158.522β = 90.00
c = 214.656γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-3000phasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History 

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-03-25
    Type: Database references