6UU4

E. coli sigma-S transcription initiation complex with a 3-nt RNA ("old" crystal soaked with GTP and dinucleotide GpA for 30 minutes)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.364 
  • R-Value Work: 0.304 

Starting Model: experimental
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Literature

Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation.

Zuo, Y.De, S.Feng, Y.Steitz, T.A.

(2020) iScience 23: 101445-101445

  • DOI: https://doi.org/10.1016/j.isci.2020.101445
  • Primary Citation of Related Structures:  
    6UTV, 6UTW, 6UTX, 6UTY, 6UTZ, 6UU0, 6UU1, 6UU2, 6UU3, 6UU4, 6UU5, 6UU6, 6UU7, 6UU8, 6UU9, 6UUA, 6UUB, 6UUC

  • PubMed Abstract: 

    In bacteria, the dissociable σ subunit of the RNA polymerase (RNAP) is responsible for initiating RNA synthesis from specific DNA sites. As nascent RNA grows, downstream DNA unwinds and is pulled into the RNAP, causing stress accumulation and initiation complex destabilization. Processive transcription elongation requires at least partial separation of the σ factor from the RNAP core enzyme. Here, we present a series of transcription complexes captured between the early initiation and elongation phases via in-crystal RNA synthesis and cleavage. Crystal structures of these complexes indicate that stress accumulation during transcription initiation is not due to clashing of the growing nascent RNA with the σ 3.2 loop, but results from scrunching of the template strand DNA that is contained inside the RNAP by the σ 3 domain. Our results shed light on how scrunching of template-strand DNA drives both abortive initiation and σ-RNAP core separation to transition transcription from initiation to elongation.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA [auth AAA],
B [auth BBB]
242Escherichia coliMutation(s): 0 
Gene Names: rpoA_1NCTC9962_06804
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7Z4
Find proteins for A0A377D9Q8 (Escherichia coli)
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UniProt GroupP0A7Z4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC [auth CCC]1,342Escherichia coliMutation(s): 0 
Gene Names: rpoBZ5560ECs4910
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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UniProt GroupP0A8V2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D [auth DDD]1,407Escherichia coliMutation(s): 0 
Gene Names: rpoCtabBb3988JW3951
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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UniProt GroupP0A8T7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE [auth EEE]90Escherichia coliMutation(s): 0 
Gene Names: rpoZb3649JW3624
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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UniProt GroupP0A800
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoSF [auth FFF]336Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoSappRkatFnurotsXsigSb2741JW5437
UniProt
Find proteins for P13445 (Escherichia coli (strain K12))
Explore P13445 
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UniProt GroupP13445
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Entity ID: 6
MoleculeChains LengthOrganismImage
Synthetic DNA 50-MER (promoter non-template strand)G [auth 111]50synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
Synthetic DNA 50-MER (promoter template strand)H [auth 222]50synthetic construct
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Entity ID: 8
MoleculeChains LengthOrganismImage
RNA 3-mer (dinucleotide GpA-primed synthesis)I [auth 333]3synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.364 
  • R-Value Work: 0.304 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.143α = 90
b = 153.432β = 90
c = 230.958γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM22778
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description