9DR1 | pdb_00009dr1

E. coli RNA polymerase consensus volume with a bound fluoride riboswitch in the ligand-bound state

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.0 of the entry. See complete history. 

Literature

Structural basis of RNA-mediated regulation of transcriptional pausing.

Porta, J.C., Ellinger, E., Liu, Y., Chauvier, A., Walter, N.G.

To be published.

Macromolecule Content 

  • Total Structure Weight: 381.36 kDa 
  • Atom Count: 26,020 
  • Modeled Residue Count: 3,232 
  • Deposited Residue Count: 3,309 
  • Unique protein chains: 4
  • Unique nucleic acid chains: 3

Macromolecules


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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaC [auth G],
D [auth H]		231Escherichia coliMutation(s): 0 
Gene Names: rpoA, Z4665, ECs4160
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7Z4
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UniProt GroupP0A7Z4
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Reference Sequence
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|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaE [auth I]1,340Escherichia coliMutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A8V2
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UniProt GroupP0A8V2
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'F [auth J]1,358Escherichia coliMutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
Explore P0A8T7 
Go to UniProtKB:  P0A8T7
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UniProt GroupP0A8T7
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Reference Sequence
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|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaG [auth K]79Escherichia coliMutation(s): 0 
Gene Names: rpoZ, Ecok1_36260, APECO1_2812
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
Explore P0A800 
Go to UniProtKB:  P0A800
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UniProt GroupP0A800
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Reference Sequence
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(by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (39-MER)30Escherichia coli
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (30-MER)30Escherichia coli
Sequence Annotations
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Reference Sequence
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Entity ID: 7
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*GP*GP*UP*AP*GP*GP*AP*GP*U)-3')H [auth R]10Escherichia coli
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG


Download:Ideal Coordinates CCD File
I [auth J]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20_4459:

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 StatesR35 GM131922

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 2.0: 2025-02-12
    Type: Coordinate replacement
    Reason: Sequence discrepancy
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Data processing, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary