6KOP

Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 9 nt


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.303 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.


    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
DNA-directed RNA polymerase subunit alpha
A, B
368Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGZ1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C
1174Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGY9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1317Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for P9WGY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGY7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E
110Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGY5
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ECF RNA polymerase sigma factor SigH
F
218Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: sigH (rpoE)
Find proteins for P9WGH9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGH9
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*GP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*A)-3')G23synthetic construct
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*GP*TP*G)-3')H21synthetic construct
Entity ID: 8
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*AP*CP*CP*CP*UP*CP*GP*A)-3')I9synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.303 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 127.371α = 90.00
b = 162.637β = 117.95
c = 133.421γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-08-12 
  • Released Date: 2020-03-11 
  • Deposition Author(s): Li, L., Zhang, Y.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31670067
Chinese Academy of SciencesChinaQYZDB-SSW-SMC005

Revision History 

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-03-18
    Type: Database references
  • Version 1.2: 2020-04-01
    Type: Database references