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- PDB-9pfv: The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CC... -

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Basic information

Entry
Database: PDB / ID: 9pfv
TitleThe cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • DNA (5'-D(P*GP*TP*C)-3')
  • DNA (53-MER)-template
  • DNA (66-MER)-non template
  • RNA polymerase sigma factor RpoD
  • WYL domain-containing protein
KeywordsTRANSCRIPTION/DNA / CCNA_03891-CCNA_01149 promoter Transcription Activation Complex / DriD / Caulobacter / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
: / WCX domain / : / WYL domain profile. / WYL domain / WYL domain / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily ...: / WCX domain / : / WYL domain profile. / WYL domain / WYL domain / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / 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, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / 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 polymerases D / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit alpha / Uncharacterized protein / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesCaulobacter vibrioides NA1000 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSingh, R.R. / Schumacher, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
Citation
Journal: Sci Adv / Year: 2026
Title: Transcription activation mechanism of a noncanonical DNA damage response pathway by the WYL-activator, DriD.
Authors: Rajiv R Singh / Amani Chinni / Emily Cannistraci / Raul Salinas / Sunny Yadav / Kevin Gozzi / Maria A Schumacher /
Abstract: DNA damage repair mechanisms are vital for cell survival. In the bacterium, , DriD is the master regulator of a unique, noncanonical DNA damage pathway. DriD binding to ssDNA, produced upon DNA ...DNA damage repair mechanisms are vital for cell survival. In the bacterium, , DriD is the master regulator of a unique, noncanonical DNA damage pathway. DriD binding to ssDNA, produced upon DNA damage, stimulates its ability to activate transcription from several promoters involved in DNA damage responses. However, the mechanism by which DriD interfaces with the RNAP holoenzyme to activate transcription from its multiple promoters has been unclear. Here, we describe cryo-EM structures of DriD-ssDNA bound to RNAP-holoenzyme and three DriD-regulated promoters. Each subunit of homodimeric DriD contains an DNA binding -terminal winged helix-turn-helix (wHTH) connected to WYL domains by a linker 3-helix bundle (3HB) module. The structures reveal a mechanism of assembly on promoters whereby DriD's 3HBs bind the RNAP α-CTD and β domains, anchoring the RNAP-holoenzyme to regulated promoters. The 3HBs form autoinhibitory contacts with DNABDs in apo DriD and therefore acts as an ssDNA-driven trigger domain, switching between DNABD-bound apo and RNAP-bound forms upon ssDNA-mediated activation. Thus, the structures reveal a unique transcription activation mechanism, likely conserved among the large family of homodimeric WYL activators.
#1: Journal: To Be Published
Title: The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex
Authors: Singh, R.R. / Schumacher, M.A.
#2: Journal: To Be Published
Title: The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-didA promoter transcription activation complex
Authors: Singh, R.R. / Schumacher, M.A.
#3: Journal: To Be Published
Title: The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex
Authors: Singh, R.R. / Schumacher, M.A.
History
DepositionJul 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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
F: RNA polymerase sigma factor RpoD
H: DNA (66-MER)-non template
I: DNA (53-MER)-template
Q: WYL domain-containing protein
L: DNA (5'-D(P*GP*TP*C)-3')
Y: DNA (5'-D(P*GP*TP*C)-3')
R: WYL domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)604,12115
Polymers603,96612
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-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE

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


Mass: 37315.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caulobacter vibrioides NA1000 (bacteria) / Strain: ML2315 (BSL1) / References: UniProt: Q9A8S9, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 151085.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caulobacter vibrioides NA1000 (bacteria) / Strain: ML2315 (BSL1) / References: UniProt: Q9AAU2, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 154467.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caulobacter vibrioides NA1000 (bacteria) / Strain: ML2315 (BSL1) / References: UniProt: Q9AAU1, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 13289.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caulobacter vibrioides NA1000 (bacteria) / Strain: ML2315 (BSL1) / References: UniProt: P58066, DNA-directed RNA polymerase

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Protein , 2 types, 3 molecules FQR

#5: Protein RNA polymerase sigma factor RpoD / Sigma-70


Mass: 72770.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides NA1000 (bacteria)
Strain: ML2315 (BSL1) / Gene: rpoD, CC_3047 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P52324
#8: Protein WYL domain-containing protein


Mass: 36212.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DeoR-family transcriptional regulator
Source: (gene. exp.) Caulobacter vibrioides NA1000 (bacteria)
Strain: ML2315 (BSL1) / Gene: CC_1095 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9A999

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DNA chain , 3 types, 4 molecules HILY

#6: DNA chain DNA (66-MER)-non template


Mass: 30196.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caulobacter vibrioides NA1000 (bacteria) / References: GenBank: 220962111
#7: DNA chain DNA (53-MER)-template


Mass: 30894.680 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caulobacter vibrioides NA1000 (bacteria) / References: GenBank: 220962111
#9: DNA chain DNA (5'-D(P*GP*TP*C)-3')


Mass: 2103.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: ssDNA / Source: (synth.) Caulobacter vibrioides NA1000 (bacteria)

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Non-polymers , 2 types, 3 molecules

#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / 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: The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex
Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Caulobacter vibrioides NA1000 (bacteria) / Strain: ML2315 (BSL1)
Buffer solutionpH: 8 / Details: 20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HClC4H11NO31
25 mMMagnesium ChlorideMgCl21
3100 mMSodium ChlorideNaCl1
41 mM1C2H6OS1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 3 uM of the reconstituted complex
Specimen supportGrid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293.15 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 magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 58.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2DigitalMicrograph3.51image acquisition
4cryoSPARC4.2.1CTF correction
7Coot9.8.96model fitting
9cryoSPARC4.2.1initial Euler assignment
10RELION5final Euler assignment
12RELION53D reconstruction
19PHENIX1.21.2-5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68485 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7ye1

7ye1


Accession code: 7ye1 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00337164
ELECTRON MICROSCOPYf_angle_d0.55150842
ELECTRON MICROSCOPYf_dihedral_angle_d15.6776068
ELECTRON MICROSCOPYf_chiral_restr0.0415847
ELECTRON MICROSCOPYf_plane_restr0.0046237

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