5E17

T. thermophilus transcription initiation complex having a RRR discriminator sequence and a nontemplate-strand length corresponding to TSS selection at position 7 (RPo-GGG-7)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection.

Winkelman, J.T.Vvedenskaya, I.O.Zhang, Y.Zhang, Y.Bird, J.G.Taylor, D.M.Gourse, R.L.Ebright, R.H.Nickels, B.E.

(2016) Science 351: 1090-1093

  • DOI: 10.1126/science.aad6881
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In bacterial transcription initiation, RNA polymerase (RNAP) selects a transcription start site (TSS) at variable distances downstream of core promoter elements. Using next-generation sequencing and unnatural amino acid-mediated protein-DNA cross-lin ...

    In bacterial transcription initiation, RNA polymerase (RNAP) selects a transcription start site (TSS) at variable distances downstream of core promoter elements. Using next-generation sequencing and unnatural amino acid-mediated protein-DNA cross-linking, we have determined, for a library of 4(10) promoter sequences, the TSS, the RNAP leading-edge position, and the RNAP trailing-edge position. We find that a promoter element upstream of the TSS, the "discriminator," participates in TSS selection, and that, as the TSS changes, the RNAP leading-edge position changes, but the RNAP trailing-edge position does not change. Changes in the RNAP leading-edge position, but not the RNAP trailing-edge position, are a defining hallmark of the "DNA scrunching" that occurs concurrent with RNA synthesis in initial transcription. We propose that TSS selection involves DNA scrunching prior to RNA synthesis.


    Organizational Affiliation

    Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA. bnickels@waksman.rutgers.edu ebright@waksman.rutgers.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alphaA, B315Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
Find proteins for Q5SHR6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SHR6
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit betaC1119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoBTTHA1813
EC: 2.7.7.6
Find proteins for Q8RQE9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q8RQE9 
Go to UniProtKB:  Q8RQE9
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omegaE99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoZTTHA1561
EC: 2.7.7.6
Find proteins for Q8RQE7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q8RQE7
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor SigAF443Thermus thermophilus HB8Mutation(s): 0 
Gene Names: sigATTHA0532
Find proteins for Q5SKW1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SKW1
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'D1524Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoCTTHA1812
EC: 2.7.7.6
Find proteins for Q8RQE8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q8RQE8
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3')G21Thermus thermophilus

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Entity ID: 7
MoleculeChainsLengthOrganism
DNA (27-MER)H27Thermus thermophilus
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 8
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*CP*CP*UP*CP*GP*A)-3')I7Thermus thermophilus
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 
B, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.007α = 90
b = 103.566β = 99.2
c = 294.935γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references