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8xa7

Cryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex

Method: ELECTRON MICROSCOPY Dmax: 153.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

Bacillus

UniProt P20429

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain A； UniProt 1–314 Chain B； UniProt 1–314 Not recorded DNA-directed RNA polymerase subunit beta × 1 （P37870） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit omega × 1 （O35011） RNA polymerase sigma factor SigA × 1 （P06224） Gene 33 protein × 1 （P06226） DNA-directed RNA polymerase subunit delta × 1 （P12464） DNA-directed RNA polymerase subunit epsilon × 1 （O31718） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.94 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 8XA7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1Z3E Crystal Structure of Spx in Complex with the C-terminal Domain of the RNA Polymerase Alpha Subunit Deposited 2005-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 245–314（70 aa） Fragment：c-terminal domain of RNA polymerase alpha subunit
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；273 K；lithium sulfate, ammonium sulfate, sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 273K
Resolution 1.50 Å R-free 0.220
3GFK Crystal structure of Bacillus subtilis Spx/RNA polymerase alpha subunit C-terminal domain complex Deposited 2009-02-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 240–314（75 aa） Fragment：Alpha C-terminal domain (alpha-CTD)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；295 K；vapor diffusion against 6% (w/v) PEG 6000, 100 mM sodium acetate, pH 5.0, 10 micromolar CuCl2, protein concentration 11.5 mg/mL, temperature 295K
Resolution 2.30 Å R-free 0.282
3IHQ Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras Deposited 2009-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 245–314（70 aa） Fragment：UNP residues 245-314
Not recorded IMD IMIDAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；273 K；25-30% PEG 4000, 0.1 M sodium citrate, 0.1 M magnesium chloride, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Resolution 1.90 Å R-free 0.278
6WVJ Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation complex Deposited 2020-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain A 1–314（314 aa）
Chain B 1–314（314 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE；Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification.
Resolution 3.36 Å
6WVK Cryo-EM structure of Bacillus subtilis RNA Polymerase in complex with HelD Deposited 2020-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–314（314 aa）
Chain B 1–314（314 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE；Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification.
Resolution 3.36 Å
7CKQ The cryo-EM structure of B. subtilis BmrR transcription activation complex Deposited 2020-07-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–314（314 aa）
Chain B 1–314（314 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 P4P TETRAPHENYLPHOSPHONIUM × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7F75 Cryo-EM structure of Spx-dependent transcription activation complex Deposited 2021-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–314（314 aa）
Chain B 1–314（314 aa）
Chain I 1–314（314 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8XA6 Cryo-EM structure of Bacillus RNAP and SPO1 gp33 complex Deposited 2023-12-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–314（314 aa）
Chain B 1–314（314 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8XA8 Cryo-EM structure of Bacillus RNAP and HelD complex Deposited 2023-12-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–314（314 aa）
Chain B 1–314（314 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.19 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPOA_BACSU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–314； UniProt 1–314 Author chain B； PDBConstruct 1–314； UniProt 1–314

DNA-directed RNA polymerase subunit beta

Bacillus

UniProt P37870

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain C； UniProt 1–1193 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （P20429） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit omega × 1 （O35011） RNA polymerase sigma factor SigA × 1 （P06224） Gene 33 protein × 1 （P06226） DNA-directed RNA polymerase subunit delta × 1 （P12464） DNA-directed RNA polymerase subunit epsilon × 1 （O31718） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.94 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 8XA7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LY7 B-flap domain of RNA polymerase (B. subtilis) Deposited 2012-09-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 784–923（140 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Pressure ambient
NMR sample composition 500 uM [U-100% 13C; U-100% 15N] b-flap, 20 mM potassium phosphate, 150 mM sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6WVK Cryo-EM structure of Bacillus subtilis RNA Polymerase in complex with HelD Deposited 2020-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–1193（1193 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE；Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification.
Resolution 3.36 Å
7CKQ The cryo-EM structure of B. subtilis BmrR transcription activation complex Deposited 2020-07-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–1193（1193 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 P4P TETRAPHENYLPHOSPHONIUM × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7F75 Cryo-EM structure of Spx-dependent transcription activation complex Deposited 2021-06-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–1193（1193 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8XA6 Cryo-EM structure of Bacillus RNAP and SPO1 gp33 complex Deposited 2023-12-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–1193（1193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8XA8 Cryo-EM structure of Bacillus RNAP and HelD complex Deposited 2023-12-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–1193（1193 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.19 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPOB_BACSU
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–1193； UniProt 1–1193

;DNA-directed RNA polymerase subunit beta' ;

Bacillus

UniProt P37871

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain D； UniProt 1–1199 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （P20429） DNA-directed RNA polymerase subunit beta × 1 （P37870） DNA-directed RNA polymerase subunit omega × 1 （O35011） RNA polymerase sigma factor SigA × 1 （P06224） Gene 33 protein × 1 （P06226） DNA-directed RNA polymerase subunit delta × 1 （P12464） DNA-directed RNA polymerase subunit epsilon × 1 （O31718） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.94 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 8XA7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WVK Cryo-EM structure of Bacillus subtilis RNA Polymerase in complex with HelD Deposited 2020-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–1199（1199 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE；Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification.
Resolution 3.36 Å
7CKQ The cryo-EM structure of B. subtilis BmrR transcription activation complex Deposited 2020-07-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–1199（1199 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 P4P TETRAPHENYLPHOSPHONIUM × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7F75 Cryo-EM structure of Spx-dependent transcription activation complex Deposited 2021-06-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 1–1199（1199 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8XA6 Cryo-EM structure of Bacillus RNAP and SPO1 gp33 complex Deposited 2023-12-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–1199（1199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8XA8 Cryo-EM structure of Bacillus RNAP and HelD complex Deposited 2023-12-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–1199（1199 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.19 Å

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

View Construct and Data Evidence
UniProt name RPOC_BACSU
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–1199； UniProt 1–1199

DNA-directed RNA polymerase subunit omega

Bacillus

UniProt O35011

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain F； UniProt 1–67 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （P20429） DNA-directed RNA polymerase subunit beta × 1 （P37870） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） RNA polymerase sigma factor SigA × 1 （P06224） Gene 33 protein × 1 （P06226） DNA-directed RNA polymerase subunit delta × 1 （P12464） DNA-directed RNA polymerase subunit epsilon × 1 （O31718） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.94 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 8XA7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WVK Cryo-EM structure of Bacillus subtilis RNA Polymerase in complex with HelD Deposited 2020-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–67（67 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE；Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification.
Resolution 3.36 Å
7CKQ The cryo-EM structure of B. subtilis BmrR transcription activation complex Deposited 2020-07-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain E 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 P4P TETRAPHENYLPHOSPHONIUM × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7F75 Cryo-EM structure of Spx-dependent transcription activation complex Deposited 2021-06-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain E 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8XA6 Cryo-EM structure of Bacillus RNAP and SPO1 gp33 complex Deposited 2023-12-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–67（67 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8XA8 Cryo-EM structure of Bacillus RNAP and HelD complex Deposited 2023-12-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–67（67 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.19 Å

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

View Construct and Data Evidence
UniProt name RPOZ_BACSU
Isoform —
PDB entities 4
Chains and sequence ranges Author chain F； PDBConstruct 1–67； UniProt 1–67

RNA polymerase sigma factor SigA

Bacillus

UniProt P06224

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain G； UniProt 1–371 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （P20429） DNA-directed RNA polymerase subunit beta × 1 （P37870） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit omega × 1 （O35011） Gene 33 protein × 1 （P06226） DNA-directed RNA polymerase subunit delta × 1 （P12464） DNA-directed RNA polymerase subunit epsilon × 1 （O31718） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.94 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 8XA7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7CKQ The cryo-EM structure of B. subtilis BmrR transcription activation complex Deposited 2020-07-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain F 1–371（371 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 P4P TETRAPHENYLPHOSPHONIUM × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7F75 Cryo-EM structure of Spx-dependent transcription activation complex Deposited 2021-06-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–371（371 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SIGA_BACSU
Isoform —
PDB entities 5
Chains and sequence ranges Author chain G； PDBConstruct 1–371； UniProt 1–371

Gene 33 protein

Bacillus phage SPO1

UniProt P06226

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain H； UniProt 1–101 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （P20429） DNA-directed RNA polymerase subunit beta × 1 （P37870） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit omega × 1 （O35011） RNA polymerase sigma factor SigA × 1 （P06224） DNA-directed RNA polymerase subunit delta × 1 （P12464） DNA-directed RNA polymerase subunit epsilon × 1 （O31718） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.94 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 8XA7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8XA6 Cryo-EM structure of Bacillus RNAP and SPO1 gp33 complex Deposited 2023-12-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain H 1–101（101 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GP33_BPSP1
Isoform —
PDB entities 6
Chains and sequence ranges Author chain H； PDBConstruct 1–101； UniProt 1–101

DNA-directed RNA polymerase subunit delta

Bacillus

UniProt P12464

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain L； UniProt 1–173 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （P20429） DNA-directed RNA polymerase subunit beta × 1 （P37870） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit omega × 1 （O35011） RNA polymerase sigma factor SigA × 1 （P06224） Gene 33 protein × 1 （P06226） DNA-directed RNA polymerase subunit epsilon × 1 （O31718） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.94 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 8XA7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2KRC Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase Deposited 2009-12-16 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–92（91 aa） Fragment：residues 2-92
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.6；301 K；Ionic strength (raw mmCIF value) 10；Pressure 1
NMR sample composition 10 mM sodium chloride-1, 50 uM sodium azide-2, 20 mM phosphate buffer-3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 10 mM sodium chloride-4, 50 uM sodium azide-5, 20 mM phosphate buffer-6, 14.29 mg/mL filamentous Pf1 bacteriophage-7, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 10 mM sodium chloride-8, 50 uM sodium azide-9, 20 mM phosphate buffer-10, 5 % polyacrylamide gel-11, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2M4K Solution structure of the delta subunit of RNA polymerase from Bacillus subtilis Deposited 2013-02-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–173（172 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.6；300 K；Ionic strength (raw mmCIF value) 10；Pressure ambient
NMR sample composition 10 % [U-100% 2H] D2O, 10 mM sodium chloride, 50 uM sodium azide, 20 mM sodium phosphate, 90 % H2O, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
4NC7 N-terminal domain of delta-subunit of RNA polymerase complexed with I3C and nickel ions Deposited 2013-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–92（91 aa） Fragment：UNP residues 2-92
Chain B 2–92（91 aa） Fragment：UNP residues 2-92
Not recorded I3C 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 1 NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290.15 K；2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；290.15 K；1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, temperature 290.15K
Resolution 2.00 Å R-free 0.259
4NC7 N-terminal domain of delta-subunit of RNA polymerase complexed with I3C and nickel ions Deposited 2013-10-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–92（91 aa） Fragment：UNP residues 2-92
Not recorded I3C 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 2 NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290.15 K；2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；290.15 K；1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, temperature 290.15K
Resolution 2.00 Å R-free 0.259
4NC7 N-terminal domain of delta-subunit of RNA polymerase complexed with I3C and nickel ions Deposited 2013-10-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 2–92（91 aa） Fragment：UNP residues 2-92
Not recorded NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290.15 K；2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；290.15 K；1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, temperature 290.15K
Resolution 2.00 Å R-free 0.259
4NC7 N-terminal domain of delta-subunit of RNA polymerase complexed with I3C and nickel ions Deposited 2013-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–92（91 aa） Fragment：UNP residues 2-92
Chain B 2–92（91 aa） Fragment：UNP residues 2-92
Not recorded I3C 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 2 NI NICKEL (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290.15 K；2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；290.15 K；1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, temperature 290.15K
Resolution 2.00 Å R-free 0.259
4NC8 N-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions Deposited 2013-10-24 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 2–92（91 aa） Fragment：UNP residues 2-92
Not recorded NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290.15 K；2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；290.15 K；1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K
Resolution 2.17 Å R-free 0.283
4NC8 N-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions Deposited 2013-10-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 2–92（91 aa） Fragment：UNP residues 2-92
Not recorded NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290.15 K；2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；290.15 K；1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K
Resolution 2.17 Å R-free 0.283
4NC8 N-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions Deposited 2013-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–92（91 aa） Fragment：UNP residues 2-92
Chain B 2–92（91 aa） Fragment：UNP residues 2-92
Not recorded NI NICKEL (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290.15 K；2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；290.15 K；1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K
Resolution 2.17 Å R-free 0.283
7F75 Cryo-EM structure of Spx-dependent transcription activation complex Deposited 2021-06-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–173（173 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8XA6 Cryo-EM structure of Bacillus RNAP and SPO1 gp33 complex Deposited 2023-12-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain L 1–173（173 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8XA8 Cryo-EM structure of Bacillus RNAP and HelD complex Deposited 2023-12-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain I 1–173（173 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.19 Å

7 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPOE_BACSU
Isoform —
PDB entities 7
Chains and sequence ranges Author chain L； PDBConstruct 1–173； UniProt 1–173

DNA-directed RNA polymerase subunit epsilon

Bacillus

UniProt O31718

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain E； UniProt 1–69 Mutation：V33I DNA-directed RNA polymerase subunit alpha × 2 （P20429） DNA-directed RNA polymerase subunit beta × 1 （P37870） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit omega × 1 （O35011） RNA polymerase sigma factor SigA × 1 （P06224） Gene 33 protein × 1 （P06226） DNA-directed RNA polymerase subunit delta × 1 （P12464） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.94 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 8XA7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WVK Cryo-EM structure of Bacillus subtilis RNA Polymerase in complex with HelD Deposited 2020-05-06 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–69（69 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE；Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification.
Resolution 3.36 Å
7CKQ The cryo-EM structure of B. subtilis BmrR transcription activation complex Deposited 2020-07-18 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain H 1–69（69 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 P4P TETRAPHENYLPHOSPHONIUM × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7F75 Cryo-EM structure of Spx-dependent transcription activation complex Deposited 2021-06-28 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain H 1–69（69 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8XA6 Cryo-EM structure of Bacillus RNAP and SPO1 gp33 complex Deposited 2023-12-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–69（69 aa）
Mutation：V33I No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å

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

View Construct and Data Evidence
UniProt name RPOY_BACSU
Isoform —
PDB entities 8
Chains and sequence ranges Author chain E； PDBConstruct 1–69； UniProt 1–69

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 8xa7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8xa7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8xa7
Deposition date deposition_date2023-12-02
Structure title titleCryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex
Keywords keywordsbacterial, phage, complex, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier47.21 Å
Radius of gyration Rg (electron density) rg_electron46.68 Å
Forward intensity I(0) i01906020000.00
Molecular weight molecular_weight364820.0 kDa
Excluded volume excluded_volume457710 ų
Envelope volume envelope_volume625720 ų
Hydration-shell volume shell_volume105710 ų
Envelope diameter envelope_diameter163.8 Å
Shell Rg shell_rg55.16 Å
Envelope Rg envelope_rg46.27 Å
Shape Rg shape_rg46.70 Å
Total Rg total_rg46.90 Å
Total atoms total_atoms51592
Residues n_residues3250
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 dmax153.4 Å
Rg (real space) rg_real46.93 Å
Rg uncertainty (real space) rg_real_error0.92 Å
I(0) (real space) i0_real1.9060e+09
I(0) uncertainty (real space) i0_real_error2.9080e+07
Rg (reciprocal space) rg_reciprocal47.20 Å
I(0) (reciprocal space) i0_reciprocal1907000000.0000
Solution quality estimate total_estimate0.8744
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary60.4 Å
Skewness Skewness skewness0.193
Kurtosis Kurtosis kurtosis-0.294
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha362700000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.901
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)