9pfq

The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

OrganismNot specified

UniProt Q9A8S9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 8 DNA 4 DNA-directed RNA polymerase subunit beta × 1 (Q9AAU2) ;DNA-directed RNA polymerase subunit beta' ; × 1 (Q9AAU1) DNA-directed RNA polymerase subunit omega × 1 (P58066) RNA polymerase sigma factor RpoD × 1 (P52324) DNA (64-MER)-non template × 1 DNA (51-MER)-template × 1 WYL domain-containing protein × 2 (Q9A999) ;DNA (5'-D(P*GP*TP*C)-3') ; × 2 MAGNESIUM ION × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOA_CAUVC
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–338; UniProt 1–338 Author chain B; PDBConstruct 1–338; UniProt 1–338

DNA-directed RNA polymerase subunit beta

OrganismNot specified

UniProt Q9AAU2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 8 DNA 4 DNA-directed RNA polymerase subunit alpha × 2 (Q9A8S9) ;DNA-directed RNA polymerase subunit beta' ; × 1 (Q9AAU1) DNA-directed RNA polymerase subunit omega × 1 (P58066) RNA polymerase sigma factor RpoD × 1 (P52324) DNA (64-MER)-non template × 1 DNA (51-MER)-template × 1 WYL domain-containing protein × 2 (Q9A999) ;DNA (5'-D(P*GP*TP*C)-3') ; × 2 MAGNESIUM ION × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOB_CAUVC
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–1356; UniProt 1–1356

;DNA-directed RNA polymerase subunit beta' ;

OrganismNot specified

UniProt Q9AAU1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 8 DNA 4 DNA-directed RNA polymerase subunit alpha × 2 (Q9A8S9) DNA-directed RNA polymerase subunit beta × 1 (Q9AAU2) DNA-directed RNA polymerase subunit omega × 1 (P58066) RNA polymerase sigma factor RpoD × 1 (P52324) DNA (64-MER)-non template × 1 DNA (51-MER)-template × 1 WYL domain-containing protein × 2 (Q9A999) ;DNA (5'-D(P*GP*TP*C)-3') ; × 2 MAGNESIUM ION × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOC_CAUVC
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–1396; UniProt 1–1396

DNA-directed RNA polymerase subunit omega

OrganismNot specified

UniProt P58066

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 8 DNA 4 DNA-directed RNA polymerase subunit alpha × 2 (Q9A8S9) DNA-directed RNA polymerase subunit beta × 1 (Q9AAU2) ;DNA-directed RNA polymerase subunit beta' ; × 1 (Q9AAU1) RNA polymerase sigma factor RpoD × 1 (P52324) DNA (64-MER)-non template × 1 DNA (51-MER)-template × 1 WYL domain-containing protein × 2 (Q9A999) ;DNA (5'-D(P*GP*TP*C)-3') ; × 2 MAGNESIUM ION × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOZ_CAUVC
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E; PDBConstruct 1–119; UniProt 1–119

RNA polymerase sigma factor RpoD

Caulobacter vibrioides NA1000

UniProt P52324

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 8 DNA 4 DNA-directed RNA polymerase subunit alpha × 2 (Q9A8S9) DNA-directed RNA polymerase subunit beta × 1 (Q9AAU2) ;DNA-directed RNA polymerase subunit beta' ; × 1 (Q9AAU1) DNA-directed RNA polymerase subunit omega × 1 (P58066) DNA (64-MER)-non template × 1 DNA (51-MER)-template × 1 WYL domain-containing protein × 2 (Q9A999) ;DNA (5'-D(P*GP*TP*C)-3') ; × 2 MAGNESIUM ION × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOD_CAUVC
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F; PDBConstruct 1–652; UniProt 1–652

WYL domain-containing protein

Caulobacter vibrioides NA1000

UniProt Q9A999

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 8 DNA 4 DNA-directed RNA polymerase subunit alpha × 2 (Q9A8S9) DNA-directed RNA polymerase subunit beta × 1 (Q9AAU2) ;DNA-directed RNA polymerase subunit beta' ; × 1 (Q9AAU1) DNA-directed RNA polymerase subunit omega × 1 (P58066) RNA polymerase sigma factor RpoD × 1 (P52324) DNA (64-MER)-non template × 1 DNA (51-MER)-template × 1 ;DNA (5'-D(P*GP*TP*C)-3') ; × 2 MAGNESIUM ION × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name Q9A999_CAUVC
Isoform —
PDB entities 8
Chains and sequence ranges Author chain Q; PDBConstruct 1–331; UniProt 1–331 Author chain R; PDBConstruct 1–331; UniProt 1–331

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id9pfq
Deposition date deposition_date2025-07-06
Structure title titleThe cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex
Keywords keywords;bapE promoter transcription activation complex, DriD, Caulobacter, TRANSCRIPTION, Non-canonical DNA Repair, TRANSCRIPTION-DNA complex ;; TRANSCRIPTION/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9pfq__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9pfq__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

9pfq__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)58.23 Å
Rg (electron density)57.43 Å
Total Rg57.45 Å
Atom count36040
Residues4574
Excluded volume632520 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9pfq__assembly_1__model_1 12-meric (12) Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (11)

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7. Citations (4)