8t00

Reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA: closed duplex DNA (rPTCc)

Method: ELECTRON MICROSCOPY Dmax: 170.9 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

Escherichia coli

UniProt A0A5B9AW69

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 × 4 DNA 2 PDB declaration: hexameric(6) Consistent with all polymer counts Chain G; UniProt 4–237 Chain H; UniProt 4–237 Not recorded DNA-directed RNA polymerase subunit beta × 1 (C3SIA7) ;DNA-directed RNA polymerase subunit beta' ; × 1 (A0A369F490) DNA (26-MER) × 1 DNA (26-MER) × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.69 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.

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

View Construct and Data Evidence
UniProt name A0A5B9AW69_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain G; PDBConstruct 1–234; UniProt 4–237 Author chain H; PDBConstruct 1–234; UniProt 4–237

DNA-directed RNA polymerase subunit beta

Escherichia coli

UniProt C3SIA7

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 × 4 DNA 2 PDB declaration: hexameric(6) Consistent with all polymer counts Chain I; UniProt 2–1341 Not recorded DNA-directed RNA polymerase subunit alpha × 2 (A0A5B9AW69) ;DNA-directed RNA polymerase subunit beta' ; × 1 (A0A369F490) DNA (26-MER) × 1 DNA (26-MER) × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.69 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.

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

View Construct and Data Evidence
UniProt name C3SIA7_ECOLX
Isoform
PDB entities 2
Chains and sequence ranges Author chain I; PDBConstruct 1–1340; UniProt 2–1341

;DNA-directed RNA polymerase subunit beta' ;

Escherichia coli

UniProt A0A369F490

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 × 4 DNA 2 PDB declaration: hexameric(6) Consistent with all polymer counts Chain J; UniProt 16–1373 Not recorded DNA-directed RNA polymerase subunit alpha × 2 (A0A5B9AW69) DNA-directed RNA polymerase subunit beta × 1 (C3SIA7) DNA (26-MER) × 1 DNA (26-MER) × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.69 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.

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

View Construct and Data Evidence
UniProt name A0A369F490_ECOLX
Isoform
PDB entities 3
Chains and sequence ranges Author chain J; PDBConstruct 1–1358; UniProt 16–1373

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 8t00

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8t00
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8t00
Deposition date deposition_date2023-05-31
Structure title titleReconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA: closed duplex DNA (rPTCc)
Keywords keywordsRNA polymerase, Negatively supercoiled DNA, Sigma-independent transcription, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier49.24
Radius of gyration Rg (electron density) rg_electron48.65
Forward intensity I(0) i01994120000.00
Molecular weight molecular_weight360010.0 kDa
Excluded volume excluded_volume446300 ų
Envelope volume envelope_volume659910 ų
Hydration-shell volume shell_volume108920 ų
Envelope diameter envelope_diameter164.3
Shell Rg shell_rg55.90
Envelope Rg envelope_rg47.73
Shape Rg shape_rg48.64
Total Rg total_rg48.90
Total atoms total_atoms25215
Residues n_residues3145
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax170.9
Rg (real space) rg_real48.92
Rg uncertainty (real space) rg_real_error1.25
I(0) (real space) i0_real1.9940e+09
I(0) uncertainty (real space) i0_real_error3.9190e+07
Rg (reciprocal space) rg_reciprocal49.24
I(0) (reciprocal space) i0_reciprocal1995000000.0000
Solution quality estimate total_estimate0.7852
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary64.1
Skewness Skewness skewness0.177
Kurtosis Kurtosis kurtosis-0.423
Angular range angular_range— – 0.1600 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha281600000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.739; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)