7EH2

Thermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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Literature

Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli .

Skalenko, K.S.Li, L.Zhang, Y.Vvedenskaya, I.O.Winkelman, J.T.Cope, A.L.Taylor, D.M.Shah, P.Ebright, R.H.Kinney, J.B.Zhang, Y.Nickels, B.E.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2106388118
  • Primary Citation of Related Structures:  
    7EH0, 7EH1, 7EH2

  • PubMed Abstract: 

    Chemical modifications of RNA 5'-ends enable "epitranscriptomic" regulation, influencing multiple aspects of RNA fate. In transcription initiation, a large inventory of substrates compete with nucleoside triphosphates for use as initiating entities, providing an ab initio mechanism for altering the RNA 5'-end. In Escherichia coli cells, RNAs with a 5'-end hydroxyl are generated by use of dinucleotide RNAs as primers for transcription initiation, "primer-dependent initiation." Here, we use massively systematic transcript end readout (MASTER) to detect and quantify RNA 5'-ends generated by primer-dependent initiation for ∼4 10 (∼1,000,000) promoter sequences in E. coli The results show primer-dependent initiation in E. coli involves any of the 16 possible dinucleotide primers and depends on promoter sequences in, upstream, and downstream of the primer binding site. The results yield a consensus sequence for primer-dependent initiation, Y TSS-2 N TSS-1 N TSS W TSS+1 , where TSS is the transcription start site, N TSS-1 N TSS is the primer binding site, Y is pyrimidine, and W is A or T. Biochemical and structure-determination studies show that the base pair (nontemplate-strand base:template-strand base) immediately upstream of the primer binding site (Y:R TSS-2 , where R is purine) exerts its effect through the base on the DNA template strand (R TSS-2 ) through interchain base stacking with the RNA primer. Results from analysis of a large set of natural, chromosomally encoded E coli promoters support the conclusions from MASTER. Our findings provide a mechanistic and structural description of how TSS-region sequence hard-codes not only the TSS position but also the potential for epitranscriptomic regulation through primer-dependent transcription initiation.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA,
B,
G [auth K],
H [auth L]
315Thermus thermophilus HB8Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5SHR6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Go to UniProtKB:  Q5SHR6
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UniProt GroupQ5SHR6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC,
I [auth M]
1,119Thermus thermophilus HB8Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D,
J [auth N]
1,524Thermus thermophilus HB8Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE,
K [auth O]
99Thermus thermophilus HB8Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigAF,
L [auth P]
443Thermus thermophilus HB8Mutation(s): 0 
Gene Names: sigATTHA0532
UniProt
Find proteins for Q5SKW1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SKW1 
Go to UniProtKB:  Q5SKW1
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UniProt GroupQ5SKW1
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (27-MER)M [auth G],
P [auth J]
27synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*CP*CP*TP*AP*G)-3')N [auth H],
Q
19synthetic construct
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Entity ID: 8
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*G)-3')O [auth I],
R
2synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.85α = 90
b = 104.2β = 98.42
c = 296.65γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31822001

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description