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6wvj

Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation complex

Method: ELECTRON MICROSCOPY Dmax: 148.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

Bacillus subtilis (strain 168)

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 Other combination Heteromer Protein × 5 DNA 2 RNA 1 PDB declaration: octameric（8） Consistent with all polymer counts Chain A； UniProt 1–314 Chain B； UniProt 1–314 Not recorded DNA-directed RNA polymerase subunit beta × 1 （A0A2J0WBQ0） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A063XB23） DNA-directed RNA polymerase subunit omega × 1 （A0A063XI46） ;DNA (5'-D(*TP*GP*TP*CP*GP*GP*GP*CP*GP*TP*CP*CP*GP*CP*GP*CP*GP*CP*C)-3') ; × 1 ;RNA (5'-R(P*GP*GP*CP*GP*CP*GP*CP*G)-3') ; × 1 ;DNA (5'-D(P*AP*CP*GP*CP*CP*CP*GP*AP*CP*A)-3') ; × 1 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 6WVJ 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
6WVK Cryo-EM structure of Bacillus subtilis RNA Polymerase in complex with HelD Deposited 2020-05-06 Different oligomeric state 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 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

Bacillus subtilis

UniProt A0A2J0WBQ0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 DNA 2 RNA 1 PDB declaration: octameric（8） Consistent with all polymer counts Chain C； UniProt 1–1193 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （P20429） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A063XB23） DNA-directed RNA polymerase subunit omega × 1 （A0A063XI46） ;DNA (5'-D(*TP*GP*TP*CP*GP*GP*GP*CP*GP*TP*CP*CP*GP*CP*GP*CP*GP*CP*C)-3') ; × 1 ;RNA (5'-R(P*GP*GP*CP*GP*CP*GP*CP*G)-3') ; × 1 ;DNA (5'-D(P*AP*CP*GP*CP*CP*CP*GP*AP*CP*A)-3') ; × 1 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 6WVJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6ZCA Structure of the B. subtilis RNA POLYMERASE in complex with HelD (monomer) Deposited 2020-06-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain X 1–1193（1193 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6ZFB Structure of the B. subtilis RNA POLYMERASE in complex with HelD (dimer) Deposited 2020-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain X 1–1193（1193 aa）
Chain x 1–1193（1193 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

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

View Construct and Data Evidence
UniProt name A0A2J0WBQ0_BACIU
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–1193； UniProt 1–1193

;DNA-directed RNA polymerase subunit beta' ;

Bacillus subtilis

UniProt A0A063XB23

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 DNA 2 RNA 1 PDB declaration: octameric（8） Consistent with all polymer counts Chain D； UniProt 1–1199 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （P20429） DNA-directed RNA polymerase subunit beta × 1 （A0A2J0WBQ0） DNA-directed RNA polymerase subunit omega × 1 （A0A063XI46） ;DNA (5'-D(*TP*GP*TP*CP*GP*GP*GP*CP*GP*TP*CP*CP*GP*CP*GP*CP*GP*CP*C)-3') ; × 1 ;RNA (5'-R(P*GP*GP*CP*GP*CP*GP*CP*G)-3') ; × 1 ;DNA (5'-D(P*AP*CP*GP*CP*CP*CP*GP*AP*CP*A)-3') ; × 1 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 6WVJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6ZCA Structure of the B. subtilis RNA POLYMERASE in complex with HelD (monomer) Deposited 2020-06-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain Y 1–1199（1199 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6ZFB Structure of the B. subtilis RNA POLYMERASE in complex with HelD (dimer) Deposited 2020-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain Y 1–1199（1199 aa）
Chain y 1–1199（1199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

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

View Construct and Data Evidence
UniProt name A0A063XB23_BACIU
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–1199； UniProt 1–1199

DNA-directed RNA polymerase subunit omega

Bacillus subtilis

UniProt A0A063XI46

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 DNA 2 RNA 1 PDB declaration: octameric（8） Consistent with all polymer counts Chain F； UniProt 1–67 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （P20429） DNA-directed RNA polymerase subunit beta × 1 （A0A2J0WBQ0） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A063XB23） ;DNA (5'-D(*TP*GP*TP*CP*GP*GP*GP*CP*GP*TP*CP*CP*GP*CP*GP*CP*GP*CP*C)-3') ; × 1 ;RNA (5'-R(P*GP*GP*CP*GP*CP*GP*CP*G)-3') ; × 1 ;DNA (5'-D(P*AP*CP*GP*CP*CP*CP*GP*AP*CP*A)-3') ; × 1 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A063XI46_BACIU
Isoform —
PDB entities 4
Chains and sequence ranges Author chain F； PDBConstruct 1–67； UniProt 1–67

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 6wvj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6wvj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6wvj
Deposition date deposition_date2020-05-06
Structure title titleCryo-EM structure of Bacillus subtilis RNA Polymerase elongation complex
Keywords keywordsDNA-DEPENDENT RNA POLYMERASE, TRANSCRIPTION, TRANSCRIPTION-DNA-RNA COMPLEX; TRANSCRIPTION/DNA/RNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier45.35 Å
Radius of gyration Rg (electron density) rg_electron45.19 Å
Forward intensity I(0) i01545060000.00
Molecular weight molecular_weight318660.0 kDa
Excluded volume excluded_volume396130 ų
Envelope volume envelope_volume551160 ų
Hydration-shell volume shell_volume97333 ų
Envelope diameter envelope_diameter160.9 Å
Shell Rg shell_rg53.03 Å
Envelope Rg envelope_rg44.64 Å
Shape Rg shape_rg45.23 Å
Total Rg total_rg45.35 Å
Total atoms total_atoms22367
Residues n_residues2839
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 dmax148.5 Å
Rg (real space) rg_real45.17 Å
Rg uncertainty (real space) rg_real_error1.05 Å
I(0) (real space) i0_real1.5450e+09
I(0) uncertainty (real space) i0_real_error2.6880e+07
Rg (reciprocal space) rg_reciprocal45.35 Å
I(0) (reciprocal space) i0_reciprocal1545000000.0000
Solution quality estimate total_estimate0.6438
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary55.1 Å
Skewness Skewness skewness0.283
Kurtosis Kurtosis kurtosis-0.207
Angular range angular_range— – 0.1750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha314400000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 0.010; Positv: 1.000; Valcen: 0.987; Smooth: 0.883
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id6wvjC01
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_id6wvjD01
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_id6wvjD02
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
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8. Citations (1)

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9. Files and Curves (10)