4Q4Z

Thermus thermophilus RNA polymerase de novo transcription initiation complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme.

Basu, R.S.Warner, B.A.Molodtsov, V.Pupov, D.Esyunina, D.Fernandez-Tornero, C.Kulbachinskiy, A.Murakami, K.S.

(2014) J Biol Chem 289: 24549-24559

  • DOI: 10.1074/jbc.M114.584037
  • Primary Citation of Related Structures:  
    4Q5S, 4Q4Z

  • PubMed Abstract: 
  • The bacterial RNA polymerase (RNAP) holoenzyme containing σ factor initiates transcription at specific promoter sites by de novo RNA priming, the first step of RNA synthesis where RNAP accepts two initiating ribonucleoside triphosphates (iNTPs) and p ...

    The bacterial RNA polymerase (RNAP) holoenzyme containing σ factor initiates transcription at specific promoter sites by de novo RNA priming, the first step of RNA synthesis where RNAP accepts two initiating ribonucleoside triphosphates (iNTPs) and performs the first phosphodiester bond formation. We present the structure of de novo transcription initiation complex that reveals unique contacts of the iNTPs bound at the transcription start site with the template DNA and also with RNAP and demonstrate the importance of these contacts for transcription initiation. To get further insight into the mechanism of RNA priming, we determined the structure of initially transcribing complex of RNAP holoenzyme with 6-mer RNA, obtained by in crystallo transcription approach. The structure highlights RNAP-RNA contacts that stabilize the short RNA transcript in the active site and demonstrates that the RNA 5'-end displaces σ region 3.2 from its position near the active site, which likely plays a key role in σ ejection during the initiation-to-elongation transition. Given the structural conservation of the RNAP active site, the mechanism of de novo RNA priming appears to be conserved in all cellular RNAPs.


    Organizational Affiliation

    From the Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, kum14@psu.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaAB315Thermus thermophilusMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for Q9Z9H6 (Thermus thermophilus)
Explore Q9Z9H6 
Go to UniProtKB:  Q9Z9H6
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
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))
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Go to UniProtKB:  Q8RQE9
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
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: 4
MoleculeChainsSequence LengthOrganismDetailsImage
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 LengthOrganismDetailsImage
RNA polymerase sigma factor SigAF423Thermus thermophilus HB8Mutation(s): 0 
Gene Names: sigATTHA0532
Find proteins for Q5SKW1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*CP*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*GP*CP*AP*GP*CP*CP*A)-3')G22N/A
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (25-MER)H27N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download CCD File 
C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
2TM
Query on 2TM

Download CCD File 
D
5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine
C10 H18 N3 O13 P3
STGUOVSTMBLHFT-ZOQUXTDFSA-N
 Ligand Interaction
ZN
Query on ZN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.256 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.487α = 90
b = 102.159β = 98.96
c = 294.719γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2014-04-15 
  • Released Date: 2014-07-30 
  • Deposition Author(s): Murakami, K.S.

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2014-10-08
    Changes: Structure summary