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6wvk

Cryo-EM structure of Bacillus subtilis RNA Polymerase in complex with HelD

Method: ELECTRON MICROSCOPY Dmax: 175.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

OrganismNot specified

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 × 7 PDB declaration: heptameric（7） 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） UPF0356 protein YkzG × 1 （O31718） DNA-directed RNA polymerase subunit omega × 1 （O35011） DNA helicase IV × 1 （O32215） 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

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 6WVK 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 ligand/ion 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 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
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 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 ligand/ion Different experimental conditions 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
8XA7 Cryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex Deposited 2023-12-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
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 2.94 Å
8XA8 Cryo-EM structure of Bacillus RNAP and HelD complex Deposited 2023-12-02 Different oligomeric state Different experimental conditions 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

OrganismNot specified

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 × 7 PDB declaration: heptameric（7） 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） UPF0356 protein YkzG × 1 （O31718） DNA-directed RNA polymerase subunit omega × 1 （O35011） DNA helicase IV × 1 （O32215） 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

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 6WVK 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 ligand/ion 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
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 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 ligand/ion Different experimental conditions 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
8XA7 Cryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex Deposited 2023-12-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
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 2.94 Å
8XA8 Cryo-EM structure of Bacillus RNAP and HelD complex Deposited 2023-12-02 Different oligomeric state Different experimental conditions 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' ;

OrganismNot specified

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 × 7 PDB declaration: heptameric（7） 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） UPF0356 protein YkzG × 1 （O31718） DNA-directed RNA polymerase subunit omega × 1 （O35011） DNA helicase IV × 1 （O32215） 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

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 6WVK 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 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 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 ligand/ion Different experimental conditions 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
8XA7 Cryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex Deposited 2023-12-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
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 2.94 Å
8XA8 Cryo-EM structure of Bacillus RNAP and HelD complex Deposited 2023-12-02 Different oligomeric state Different experimental conditions 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

UPF0356 protein YkzG

OrganismNot specified

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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count Chain E； UniProt 1–69 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） DNA helicase IV × 1 （O32215） 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

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 6WVK 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 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 oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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
8XA7 Cryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex Deposited 2023-12-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
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 2.94 Å

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

View Construct and Data Evidence
UniProt name YKZG_BACSU
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E； PDBConstruct 1–69； UniProt 1–69

DNA-directed RNA polymerase subunit omega

OrganismNot specified

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 × 7 PDB declaration: heptameric（7） 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） UPF0356 protein YkzG × 1 （O31718） DNA helicase IV × 1 （O32215） 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

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 6WVK 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 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 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 ligand/ion Different experimental conditions 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
8XA7 Cryo-EM structure of Bacillus subtilis RNAP,sigA and SPO1 gp33 complex Deposited 2023-12-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
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 2.94 Å
8XA8 Cryo-EM structure of Bacillus RNAP and HelD complex Deposited 2023-12-02 Different oligomeric state Different experimental conditions 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 5
Chains and sequence ranges Author chain F； PDBConstruct 1–67； UniProt 1–67

DNA helicase IV

OrganismNot specified

UniProt O32215

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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count Chain H； UniProt 1–774 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） UPF0356 protein YkzG × 1 （O31718） DNA-directed RNA polymerase subunit omega × 1 （O35011） 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

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 6WVK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8XA8 Cryo-EM structure of Bacillus RNAP and HelD complex Deposited 2023-12-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain H 1–774（774 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

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

View Construct and Data Evidence
UniProt name HELD_BACSU
Isoform —
PDB entities 6
Chains and sequence ranges Author chain H； PDBConstruct 1–774； UniProt 1–774

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 6wvk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6wvk
Download Download
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6wvk
Deposition date deposition_date2020-05-06
Structure title titleCryo-EM structure of Bacillus subtilis RNA Polymerase in complex with HelD
Keywords keywordsRNA POLYMERASE, TRANSFERASE-HELD 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_guinier52.72 Å
Radius of gyration Rg (electron density) rg_electron52.35 Å
Forward intensity I(0) i02275710000.00
Molecular weight molecular_weight401030.0 kDa
Excluded volume excluded_volume503110 ų
Envelope volume envelope_volume743940 ų
Hydration-shell volume shell_volume115310 ų
Envelope diameter envelope_diameter171.3 Å
Shell Rg shell_rg58.57 Å
Envelope Rg envelope_rg51.11 Å
Shape Rg shape_rg52.37 Å
Total Rg total_rg52.47 Å
Total atoms total_atoms28227
Residues n_residues3631
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 dmax175.1 Å
Rg (real space) rg_real52.55 Å
Rg uncertainty (real space) rg_real_error1.56 Å
I(0) (real space) i0_real2.2760e+09
I(0) uncertainty (real space) i0_real_error4.2550e+07
Rg (reciprocal space) rg_reciprocal52.84 Å
I(0) (reciprocal space) i0_reciprocal2277000000.0000
Solution quality estimate total_estimate0.8773
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary64.2 Å
Skewness Skewness skewness0.211
Kurtosis Kurtosis kurtosis-0.417
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha307100000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.886
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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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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6wvkC01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily150 — RNA polymerase II, Rpb2 subunit, wall domain
Domain ID domain_id6wvkD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily100 — RNA polymerase Rpb1, domain 3
Domain ID domain_id6wvkD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology132 — Topoisomerase I; Chain A, domain 4
Homologous superfamily homologous superfamily30 — RNA polymerase Rpb1 funnel domain
Domain ID domain_id6wvkH01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (1)

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9. Files and Curves (10)