6JNX

Cryo-EM structure of a Q-engaged arrested complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis of Q-dependent transcription antitermination.

Shi, J., Gao, X., Tian, T., Yu, Z., Gao, B., Wen, A., You, L., Chang, S., Zhang, X., Zhang, Y., Feng, Y.

(2019) Nat Commun 10: 2925-2925

  • DOI: https://doi.org/10.1038/s41467-019-10958-8
  • Primary Citation of Related Structures:  
    6JNX, 6JNY

  • PubMed Abstract: 

    • Bacteriophage Q protein engages σ-dependent paused RNA polymerase (RNAP) by binding to a DNA site embedded in late gene promoter and renders RNAP resistant to termination signals. Here, we report a single-particle cryo-electron microscopy (cryo-EM) structure of an intact Q-engaged arrested complex ...

    Bacteriophage Q protein engages σ-dependent paused RNA polymerase (RNAP) by binding to a DNA site embedded in late gene promoter and renders RNAP resistant to termination signals. Here, we report a single-particle cryo-electron microscopy (cryo-EM) structure of an intact Q-engaged arrested complex. The structure reveals key interactions responsible for σ-dependent pause, Q engagement, and Q-mediated transcription antitermination. The structure shows that two Q protomers (Q I and Q II ) bind to a direct-repeat DNA site and contact distinct elements of the RNA exit channel. Notably, Q I forms a narrow ring inside the RNA exit channel and renders RNAP resistant to termination signals by prohibiting RNA hairpin formation in the RNA exit channel. Because the RNA exit channel is conserved among all multisubunit RNAPs, it is likely to serve as an important contact site for regulators that modify the elongation properties of RNAP in other organisms, as well.

    Organizational Affiliation: 

    Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China. yufengjay@zju.edu.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
329Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoA, pez, phs, sez, b3295, JW3257
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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UniProt GroupP0A7Z4
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,342Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,407Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoC, tabB, b3988, JW3951
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega91Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoZ, b3649, JW3624
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoD613Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoD, alt, b3067, JW3039
UniProt
Find proteins for P00579 (Escherichia coli (strain K12))
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UniProt GroupP00579
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Antiterminator Q proteinJ [auth P],
K [auth Q]		162Enterobacteria phage SfIMutation(s): 0 
Gene Names: Q, SfI_0061
UniProt
Find proteins for M1FPN0 (Enterobacteria phage SfI)
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (63-MER)G [auth N]63Enterobacteria phage P21
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Entity ID: 7
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*AP*UP*AP*AP*GP*GP*UP*GP*GP*GP*GP*UP*UP*AP*GP*UP*GP*A)-3')H [auth R]18Enterobacteria phage P21
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (63-MER)I [auth T]63Enterobacteria phage P21
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
M [auth D],
N [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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L [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other