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

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Basic information

Entry
Database: PDB / ID: 9pfq
TitleThe cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • DNA (5'-D(P*GP*TP*C)-3')
  • DNA (51-MER)-template
  • DNA (64-MER)-non template
  • RNA polymerase sigma factor RpoD
  • WYL domain-containing protein
KeywordsTRANSCRIPTION/DNA / bapE promoter transcription activation complex / DriD / Caulobacter / TRANSCRIPTION / Non-canonical DNA Repair / 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, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / 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 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 / 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 / DNA-directed RNA polymerase, insert domain superfamily / 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 / 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: 4.24 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: 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.
#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-CCNA_03891/CCNA_01149 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
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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 (64-MER)-non template
I: DNA (51-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)598,56115
Polymers598,40612
Non-polymers1553
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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) / Strain (production host): BL21(DE3) / 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
Source: (gene. exp.) Caulobacter vibrioides NA1000 (bacteria)
Strain: ML2315 (BSL1) / Gene: CC_1095 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q9A999

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DNA chain , 3 types, 4 molecules HILY

#6: DNA chain DNA (64-MER)-non template


Mass: 27645.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caulobacter vibrioides NA1000 (bacteria) / References: GenBank: 220962111
#7: DNA chain DNA (51-MER)-template


Mass: 27885.748 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: Single Strand DNA / 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-bapE 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: 59 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
4cryoSPARC4.3.0CTF correction
7Coot9.8.96model fitting
9PHENIX1.21.2-5419model refinement
10cryoSPARC4.3.0initial Euler assignment
11cryoSPARC4.6.2final Euler assignment
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13962 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7ye1

7ye1


Accession code: 7ye1 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 4.24 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00336887
ELECTRON MICROSCOPYf_angle_d0.6350482
ELECTRON MICROSCOPYf_dihedral_angle_d15.9966025
ELECTRON MICROSCOPYf_chiral_restr0.0425822
ELECTRON MICROSCOPYf_plane_restr0.0056204

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