6AWD

Structure of 30S (S1 depleted) ribosomal subunit and RNA polymerase complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.3 of the entry. See complete history


Literature

Structure of RNA polymerase bound to ribosomal 30S subunit.

Demo, G.Rasouly, A.Vasilyev, N.Svetlov, V.Loveland, A.B.Diaz-Avalos, R.Grigorieff, N.Nudler, E.Korostelev, A.A.

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.28560
  • Primary Citation of Related Structures:  
    6AWB, 6AWC, 6AWD

  • PubMed Abstract: 

    In bacteria, mRNA transcription and translation are coupled to coordinate optimal gene expression and maintain genome stability. Coupling is thought to involve direct interactions between RNA polymerase (RNAP) and the translational machinery. We present cryo-EM structures of E. coli RNAP core bound to the small ribosomal 30S subunit. The complex is stable under cell-like ionic conditions, consistent with functional interaction between RNAP and the 30S subunit. The RNA exit tunnel of RNAP aligns with the Shine-Dalgarno-binding site of the 30S subunit. Ribosomal protein S1 forms a wall of the tunnel between RNAP and the 30S subunit, consistent with its role in directing mRNAs onto the ribosome. The nucleic-acid-binding cleft of RNAP samples distinct conformations, suggesting different functional states during transcription-translation coupling. The architecture of the 30S•RNAP complex provides a structural basis for co-localization of the transcriptional and translational machineries, and inform future mechanistic studies of coupled transcription and translation.


  • Organizational Affiliation

    RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaB [auth 01],
C [auth 02]
229Escherichia coliMutation(s): 0 
Gene Names: rpoAZ4665ECs4160
EC: 2.7.7.6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaD [auth 03]1,340Escherichia coliMutation(s): 0 
Gene Names: rpoBECS88_4448
EC: 2.7.7.6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'E [auth 04]1,369Escherichia coliMutation(s): 0 
Gene Names: rpoCZ5561ECs4911
EC: 2.7.7.6
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaF [auth 05]59Escherichia coliMutation(s): 0 
Gene Names: rpoZECS88_4064
EC: 2.7.7.6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2G [auth E]218Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3H [auth F]206Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4I [auth G]205Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5J [auth H]157Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6K [auth I]100Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7L [auth J]151Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8M [auth K]129Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9N [auth L]127Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10O [auth M]98Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11P [auth N]116Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12Q [auth O]123Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13R [auth P]114Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14S [auth Q]100Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15T [auth R]88Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16U [auth S]82Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17V [auth T]80Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18W [auth U]65Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19X [auth V]79Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20Y [auth W]85Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21Z [auth X]65Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNA1,539Escherichia coli
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN9.11
MODEL REFINEMENTRSRef
MODEL REFINEMENTPHENIX1.11

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM106105
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107465
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107329

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Database references
  • Version 2.0: 2017-12-06
    Changes: Author supporting evidence, Polymer sequence
  • Version 2.1: 2018-07-18
    Changes: Data collection
  • Version 2.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.3: 2024-03-13
    Changes: Data collection, Database references