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9pga

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

Method: ELECTRON MICROSCOPY Dmax: 194.4 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 × 8 DNA 4 PDB declaration: 12-meric（12） 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 (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 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 3.98 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.

Other PDB Difference from Current Entry 9PGA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9PFQ The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex Deposited 2025-07-06 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 12-meric
Chain A 1–338（338 aa）
Chain B 1–338（338 aa）
Not recorded 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 4.24 Å
9PFV The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex Deposited 2025-07-06 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: dodecameric
Chain A 1–338（338 aa）
Chain B 1–338（338 aa）
Not recorded 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 3.70 Å
9PGH The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex Deposited 2025-07-07 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain A 1–338（338 aa）
Chain B 1–338（338 aa）
Not recorded 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
9ZUM Structure of the Caulobacter crescentus RNAP alpha-CTD bound to AT rich DNA Deposited 2025-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 251–329（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1-2% PEG 2000 MME, 1 mM Ammonium sulphate, 20 mM sodium acetate pH 5.5
Resolution 2.43 Å R-free 0.242
9ZUM Structure of the Caulobacter crescentus RNAP alpha-CTD bound to AT rich DNA Deposited 2025-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 251–329（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1-2% PEG 2000 MME, 1 mM Ammonium sulphate, 20 mM sodium acetate pH 5.5
Resolution 2.43 Å R-free 0.242
9ZUM Structure of the Caulobacter crescentus RNAP alpha-CTD bound to AT rich DNA Deposited 2025-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 251–329（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1-2% PEG 2000 MME, 1 mM Ammonium sulphate, 20 mM sodium acetate pH 5.5
Resolution 2.43 Å R-free 0.242
9ZUM Structure of the Caulobacter crescentus RNAP alpha-CTD bound to AT rich DNA Deposited 2025-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 251–329（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1-2% PEG 2000 MME, 1 mM Ammonium sulphate, 20 mM sodium acetate pH 5.5
Resolution 2.43 Å R-free 0.242
9ZUM Structure of the Caulobacter crescentus RNAP alpha-CTD bound to AT rich DNA Deposited 2025-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 251–329（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1-2% PEG 2000 MME, 1 mM Ammonium sulphate, 20 mM sodium acetate pH 5.5
Resolution 2.43 Å R-free 0.242

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 × 8 DNA 4 PDB declaration: 12-meric（12） 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 (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 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 3.98 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.

Other PDB Difference from Current Entry 9PGA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9PFQ The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex Deposited 2025-07-06 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 12-meric
Chain C 1–1356（1356 aa）
Not recorded 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 4.24 Å
9PFV The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex Deposited 2025-07-06 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: dodecameric
Chain C 1–1356（1356 aa）
Not recorded 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 3.70 Å
9PGH The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex Deposited 2025-07-07 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–1356（1356 aa）
Not recorded 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

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 × 8 DNA 4 PDB declaration: 12-meric（12） 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 (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 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 3.98 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.

Other PDB Difference from Current Entry 9PGA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9PFQ The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex Deposited 2025-07-06 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 12-meric
Chain D 1–1396（1396 aa）
Not recorded 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 4.24 Å
9PFV The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex Deposited 2025-07-06 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: dodecameric
Chain D 1–1396（1396 aa）
Not recorded 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 3.70 Å
9PGH The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex Deposited 2025-07-07 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain D 1–1396（1396 aa）
Not recorded 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

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 × 8 DNA 4 PDB declaration: 12-meric（12） 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 (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 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 3.98 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.

Other PDB Difference from Current Entry 9PGA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9PFQ The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex Deposited 2025-07-06 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 12-meric
Chain E 1–119（119 aa）
Not recorded 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 4.24 Å
9PFV The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex Deposited 2025-07-06 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: dodecameric
Chain E 1–119（119 aa）
Not recorded 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 3.70 Å
9PGH The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex Deposited 2025-07-07 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain E 1–119（119 aa）
Not recorded 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

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 × 8 DNA 4 PDB declaration: 12-meric（12） 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 (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 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 3.98 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.

Other PDB Difference from Current Entry 9PGA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9PFQ The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex Deposited 2025-07-06 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 12-meric
Chain F 1–652（652 aa）
Not recorded 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 4.24 Å
9PFV The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex Deposited 2025-07-06 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: dodecameric
Chain F 1–652（652 aa）
Not recorded 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 3.70 Å
9PGH The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex Deposited 2025-07-07 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain F 1–652（652 aa）
Not recorded 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

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

WYL domain-containing protein

Caulobacter vibrioides NA1000

UniProt Q9A999

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 × 8 DNA 4 PDB declaration: 12-meric（12） Consistent with all polymer counts Chain Q； UniProt 1–331 Chain R； UniProt 1–331 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） 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 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 3.98 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.

Other PDB Difference from Current Entry 9PGA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7TZV Structure of DriD C-domain bound to 9mer ssDNA Deposited 2022-02-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain A 138–331（194 aa）
Chain M 138–331（194 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；297 K；0.1 M MES pH 6.5, 0.1 M Imidazole, 20% PEG 8000
Resolution 1.65 Å R-free 0.223
7U02 Structure of the C. crescentus DriD C-domain bound to ssDNA Deposited 2022-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain B 138–331（194 aa）
Chain M 138–331（194 aa）
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；297 K；Ammonium sulphate
Resolution 2.48 Å R-free 0.279
9CU3 Allosteric mechanism of DriD transcription activator Deposited 2024-07-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 82–331（250 aa）
Chain B 82–331（250 aa）
Not recorded GOL GLYCEROL × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298.15 K；Ammonium sulfate dibasic, sodium cacodylate trihydrate
Resolution 1.90 Å R-free 0.231
9PFQ The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex Deposited 2025-07-06 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 12-meric
Chain Q 1–331（331 aa）
Chain R 1–331（331 aa）
Not recorded 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 4.24 Å
9PFV The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex Deposited 2025-07-06 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: dodecameric
Chain Q 1–331（331 aa）
Chain R 1–331（331 aa）
Not recorded 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 3.70 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9pga

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9pga
Download Download
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9pga
Deposition date deposition_date2025-07-07
Structure title titleThe cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-didA promoter transcription activation complex
Keywords keywords;didA 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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier58.02 Å
Radius of gyration Rg (electron density) rg_electron57.25 Å
Forward intensity I(0) i04117150000.00
Molecular weight molecular_weight509820.0 kDa
Excluded volume excluded_volume626630 ų
Envelope volume envelope_volume1022000 ų
Hydration-shell volume shell_volume143430 ų
Envelope diameter envelope_diameter198.0 Å
Shell Rg shell_rg63.02 Å
Envelope Rg envelope_rg56.84 Å
Shape Rg shape_rg57.28 Å
Total Rg total_rg57.28 Å
Total atoms total_atoms35717
Residues n_residues4546
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax194.4 Å
Rg (real space) rg_real57.86 Å
Rg uncertainty (real space) rg_real_error1.40 Å
I(0) (real space) i0_real4.1170e+09
I(0) uncertainty (real space) i0_real_error7.4760e+07
Rg (reciprocal space) rg_reciprocal58.13 Å
I(0) (reciprocal space) i0_reciprocal4119000000.0000
Solution quality estimate total_estimate0.8659
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary72.0 Å
Skewness Skewness skewness0.287
Kurtosis Kurtosis kurtosis-0.317
Angular range angular_range— – 0.1350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha623800000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.775
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (11)

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8. Citations (4)

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9. Files and Curves (10)