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- PDB-12ce: Head-on RNAP-RNAP Collision: 26 bp distance -

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Basic information

Entry
Database: PDB / ID: 12ce
TitleHead-on RNAP-RNAP Collision: 26 bp distance
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • Non-template strand homopolymer
  • RNA strand
  • Template strand homopolymer
KeywordsTRANSCRIPTION / RNA polymerase / E. Coli
Function / homology
Function and homology information


RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / nitrate assimilation / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / cell motility ...RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / nitrate assimilation / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / cell motility / DNA-templated transcription elongation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit beta-prime ...DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb1, domain 1 / RNA polymerases D / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, funnel domain superfamily / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsWatters, J.W. / Alushin, G.M. / Liu, S. / Mueller, A.U. / Ju, X. / Chuquimarca, S.J. / Ye, H.J. / Darst, S.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateG-2024-22709 United States
CitationJournal: To Be Published
Title: Structural principles of transcriptional collisions
Authors: Watters, J.W. / Alushin, G.M. / Liu, S. / Mueller, A.U. / Ju, X. / Chuquimarca, S.J. / Ye, H.J. / Darst, S.A.
History
DepositionMar 26, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2026Provider: repository / Type: Initial release
Revision 1.0Nov 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: Non-template strand homopolymer
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
R: RNA strand
T: Template strand homopolymer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)415,29811
Polymers415,1438
Non-polymers1553
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 2 types, 2 molecules NT

#1: DNA chain Non-template strand homopolymer


Mass: 10707.772 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Non-template DNA strand modeled as a dGTP homopolymer due to the heterogeneity of the sequence of the complex. Addded a string of dCTPs that are not present in the structure to maintain the gap
Source: (synth.) synthetic construct (others)
#7: DNA chain Template strand homopolymer


Mass: 9498.041 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Template strand modeled as a dCTP homopolymer due to the heterogeneity of the sequence of the complex.
Source: (synth.) synthetic construct (others)

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE

#2: Protein DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 36558.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 150820.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
Production host: Escherichia coli (E. coli) / References: UniProt: P0A8V2, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 156306.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal 3C cleavage site to remove His10 tag / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, tabB, b3988, JW3951 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8T7, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 10249.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, b3649, JW3624 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A800, DNA-directed RNA polymerase

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RNA chain , 1 types, 1 molecules R

#6: RNA chain RNA strand


Mass: 4442.718 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA in the transcription RNA-DNA hybrid including two backtracked bases. Modeled as a GTP homopolymer due to the heterogeneity of the sequence of the complex.
Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 3 molecules

#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Head-On RNAP-RNAP Collision Elongation Complex: 26 base pairs inter-RNAP distance.
Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8 / Details: pH 7.8 at room temperature
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris AcetateTris-OAc1
250 mMPotassium AcetateKOAc1
35 mMMagnesium AcetateMgOAc1
42.5 mMDithiothreitolDTT1
51.5 mMFos-Choline81
60.1 mg/mLHeparin1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Concentrated to ~4 uM DNA template
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1.4 sec. / Electron dose: 48.79 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 20080
EM imaging opticsEnergyfilter name: GIF Bioquantum
Image scansWidth: 4092 / Height: 5760

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.0particle selection
2SerialEMimage acquisition
4cryoSPARC4.7.0CTF correction
7ISOLDE1.10.0model fitting
8Coot0.8.7model fitting
10PHENIX"2.0_5936"model refinement
11cryoSPARC4.7.0initial Euler assignment
12cryoSPARC4.7.0final Euler assignment
13cryoSPARC4.7.0classification
14cryoSPARC4.7.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1801942
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 219123 / Algorithm: FOURIER SPACE
Details: Particles were symmetry expanded and then refined with a mask representative of one of the two complexes.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1 / Accession code: 6RIP / Initial refinement model-ID: 1 / PDB-ID: 6RIP

6rip

/ Source name: PDB / Type: experimental model

IDPdb chain-IDChain-ID
1AA
2BB
3CC
4DD
5EE
6NN
7TT
8RR

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