9pgh

The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex

Method: ELECTRON MICROSCOPY Dmax: 176.8 Å Quality: GOOD

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric(8) Consistent with all polymer counts Chain A; UniProt 1–338 Chain B; UniProt 1–338 Not recorded 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 (55-MER)-non template × 1 DNA (43-MER)-template × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.54 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric(8) Consistent with all polymer counts Chain C; UniProt 1–1356 Not recorded 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 (55-MER)-non template × 1 DNA (43-MER)-template × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.54 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric(8) Consistent with all polymer counts Chain D; UniProt 1–1396 Not recorded 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 (55-MER)-non template × 1 DNA (43-MER)-template × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.54 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric(8) Consistent with all polymer counts Chain E; UniProt 1–119 Not recorded 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 (55-MER)-non template × 1 DNA (43-MER)-template × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.54 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric(8) Consistent with all polymer counts Chain F; UniProt 1–652 Not recorded 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 (55-MER)-non template × 1 DNA (43-MER)-template × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.54 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9pgh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9pgh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9pgh
Deposition date deposition_date2025-07-07
Structure title titleThe cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex
Keywords keywordsCCNA_03891-CCNA_01149 promoter complex, DriD, Caulobacter, RNA Polymerase, Transcription, TRANSCRIPTION-DNA complex; TRANSCRIPTION/DNA
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier53.23
Radius of gyration Rg (electron density) rg_electron52.39
Forward intensity I(0) i02916380000.00
Molecular weight molecular_weight428840.0 kDa
Excluded volume excluded_volume527850 ų
Envelope volume envelope_volume831800 ų
Hydration-shell volume shell_volume126980 ų
Envelope diameter envelope_diameter190.4
Shell Rg shell_rg59.39
Envelope Rg envelope_rg52.23
Shape Rg shape_rg52.40
Total Rg total_rg52.53
Total atoms total_atoms30040
Residues n_residues3815
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax176.8
Rg (real space) rg_real53.08
Rg uncertainty (real space) rg_real_error1.15
I(0) (real space) i0_real2.9160e+09
I(0) uncertainty (real space) i0_real_error4.9260e+07
Rg (reciprocal space) rg_reciprocal53.35
I(0) (reciprocal space) i0_reciprocal2917000000.0000
Solution quality estimate total_estimate0.8666
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary64.8
Skewness Skewness skewness0.284
Kurtosis Kurtosis kurtosis-0.232
Angular range angular_range— – 0.1500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha506800000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.848

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

8. Citations (4)

9. Files and Curves (10)