6KON

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

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 U S A 117: 5801-5809

  • DOI: 10.1073/pnas.1920747117
  • Structures With Same Primary Citation

  • 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

    Department of Chemistry, Rutgers University, Piscataway, NJ 08854.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B
368Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoARv3457cMTCY13E12.10c
EC: 2.7.7.6
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGZ1

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C
1174Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoBRv0667MTCI376.08c
EC: 2.7.7.6
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGY9

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1317Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoCRv0668MTCI376.07c
EC: 2.7.7.6
Find proteins for P9WGY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGY7

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E
110Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoZRv1390MTCY21B4.07
EC: 2.7.7.6
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGY5

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ECF RNA polymerase sigma factor SigH
F
218Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: sigHrpoERv3223cMTCY07D11.03
Find proteins for P9WGH9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGH9

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*TP*TP*GP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*C)-3')G23synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*GP*TP*G)-3')H20synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 8
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*UP*CP*GP*A)-3')I5synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.33α = 90
b = 161.219β = 117.78
c = 129.469γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



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
    Changes: Database references
  • Version 1.2: 2020-04-01
    Changes: Database references