4G7Z

Crystal structure of Thermus thermophilus transcription initiation complex containing 5-BrU at template-strand position +1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.81 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural basis of transcription initiation.

Zhang, Y.Feng, Y.Chatterjee, S.Tuske, S.Ho, M.X.Arnold, E.Ebright, R.H.

(2012) Science 338: 1076-1080

  • DOI: https://doi.org/10.1126/science.1227786
  • Primary Citation of Related Structures:  
    4G7H, 4G7O, 4G7Z

  • PubMed Abstract: 

    During transcription initiation, RNA polymerase (RNAP) binds and unwinds promoter DNA to form an RNAP-promoter open complex. We have determined crystal structures at 2.9 and 3.0 Å resolution of functional transcription initiation complexes comprising Thermus thermophilus RNA polymerase, σ(A), and a promoter DNA fragment corresponding to the transcription bubble and downstream double-stranded DNA of the RNAP-promoter open complex. The structures show that σ recognizes the -10 element and discriminator element through interactions that include the unstacking and insertion into pockets of three DNA bases and that RNAP recognizes the -4/+2 region through interactions that include the unstacking and insertion into a pocket of the +2 base. The structures further show that interactions between σ and template-strand single-stranded DNA (ssDNA) preorganize template-strand ssDNA to engage the RNAP active center.


  • Organizational Affiliation

    Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.


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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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 factorF,
L [auth P]
443Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoDTTHA0532
UniProt
Find proteins for Q5SKW1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SKW1
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Entity ID: 6
MoleculeChains LengthOrganismImage
5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3'M [auth H],
O [auth R]
27N/A
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Entity ID: 7
MoleculeChains LengthOrganismImage
5'-D(*CP*CP*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*(BRU)P*CP*GP*AP*GP*GP*G)-3'N [auth G],
P [auth Q]
21N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.81 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.465α = 90
b = 103.59β = 98.53
c = 296.507γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2012-11-07
    Changes: Database references
  • Version 1.2: 2012-12-12
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description