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8g8z

Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand

Method: ELECTRON MICROSCOPY Dmax: 154.3 Å Quality: GOOD
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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 Other combination Heteromer Protein × 5 DNA 2 RNA 1 PDB declaration: octameric（8） Consistent with all polymer counts Chain G； UniProt 1–234 Chain H； UniProt 1–234 Not recorded DNA (39-MER) × 1 DNA (31-MER) × 1 DNA-directed RNA polymerase subunit omega × 1 （A0A1X3IVJ5） RNA (48-MER) × 1 DNA-directed RNA polymerase subunit beta × 1 （C3SIA7） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A369F490） PRF 7-DEAZA-7-AMINOMETHYL-GUANINE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；Vitrification was carried out in a chamber with the temperature set to 4 C. Resolution 4.30 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 8G8Z Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8G00 Cryo-EM structure of 3DVA component 0 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand Deposited 2023-01-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 1–235（235 aa）
Chain H 1–239（239 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION WAS CARRIED OUT IN A CHAMBER WITH THE TEMPERATURE SET TO 4 DEGREES CELSIUS.
Resolution 3.40 Å
8G1S Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand Deposited 2023-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 1–235（235 aa）
Chain H 1–235（235 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM TRIS-HCl, pH 7.5; 100 mM potassium chloride, 1mM
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification was carried out in a chamber with the temperature set to 4 C.
Resolution 3.70 Å
8G2W Cryo-EM structure of 3DVA component 2 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand Deposited 2023-02-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 1–234（234 aa）
Chain H 1–234（234 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION WAS CARRIED OUT IN A CHAMBER WITH THE TEMPERATURE SET TO 4 DEGREES CELSIUS.
Resolution 3.70 Å
8G4W Cryo-EM consensus structure of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand Deposited 2023-02-10 Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 1–234（234 aa）
Chain H 1–234（234 aa）
Not recorded PRF 7-DEAZA-7-AMINOMETHYL-GUANINE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION WAS CARRIED OUT IN A CHAMBER WITH THE TEMPERATURE SET TO 4 DEGREES CELSIUS.
Resolution 3.80 Å
8G7E Cryo-EM structure of 3DVA component 0 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand Deposited 2023-02-16 Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 1–234（234 aa）
Chain H 1–234（234 aa）
Not recorded PRF 7-DEAZA-7-AMINOMETHYL-GUANINE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION WAS CARRIED OUT IN A CHAMBER WITH THE TEMPERATURE SET TO 4 DEGREES CELSIUS.
Resolution 3.90 Å
8PBL E. coli RNA polymerase elongation complex stalled at thymine dimer lesion Deposited 2023-06-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain D 1–235（235 aa）
Chain E 1–235（235 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8T00 Reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA: closed duplex DNA (rPTCc) Deposited 2023-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain G 4–237（234 aa）
Chain H 4–237（234 aa）
Not recorded 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
9N07 Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1 state Deposited 2025-01-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain G 4–237（234 aa）
Chain H 4–237（234 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9N11 Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1.5 state Deposited 2025-01-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain G 4–237（234 aa）
Chain H 4–237（234 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.29 Å

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 3
Chains and sequence ranges Author chain G； PDBConstruct 1–234； UniProt 1–234 Author chain H； PDBConstruct 1–234； UniProt 1–234

DNA-directed RNA polymerase subunit omega

Escherichia coli

UniProt A0A1X3IVJ5

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 K； UniProt 1–80 Not recorded DNA (39-MER) × 1 DNA (31-MER) × 1 DNA-directed RNA polymerase subunit alpha × 2 （A0A5B9AW69） RNA (48-MER) × 1 DNA-directed RNA polymerase subunit beta × 1 （C3SIA7） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A369F490） PRF 7-DEAZA-7-AMINOMETHYL-GUANINE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；Vitrification was carried out in a chamber with the temperature set to 4 C. Resolution 4.30 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 8G8Z Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6VZ7 Escherichia coli transcription-translation complex C1 (TTC-C1) containing a 27 nt long mRNA spacer, NusG, and fMet-tRNAs at P-site and E-site Deposited 2020-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 56 PDB declaration: 65-meric
Chain AF 2–84（83 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
8G1S Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand Deposited 2023-02-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain K 1–80（80 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM TRIS-HCl, pH 7.5; 100 mM potassium chloride, 1mM
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification was carried out in a chamber with the temperature set to 4 C.
Resolution 3.70 Å

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

View Construct and Data Evidence
UniProt name A0A1X3IVJ5_ECOLX
Isoform —
PDB entities 4
Chains and sequence ranges Author chain K； PDBConstruct 1–80； UniProt 1–80

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 Other combination Heteromer Protein × 5 DNA 2 RNA 1 PDB declaration: octameric（8） Consistent with all polymer counts Chain I； UniProt 2–1341 Not recorded DNA (39-MER) × 1 DNA (31-MER) × 1 DNA-directed RNA polymerase subunit alpha × 2 （A0A5B9AW69） DNA-directed RNA polymerase subunit omega × 1 （A0A1X3IVJ5） RNA (48-MER) × 1 ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A369F490） PRF 7-DEAZA-7-AMINOMETHYL-GUANINE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；Vitrification was carried out in a chamber with the temperature set to 4 C. Resolution 4.30 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 8G8Z Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8G2W Cryo-EM structure of 3DVA component 2 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand Deposited 2023-02-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 2–1341（1340 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION WAS CARRIED OUT IN A CHAMBER WITH THE TEMPERATURE SET TO 4 DEGREES CELSIUS.
Resolution 3.70 Å
8G4W Cryo-EM consensus structure of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand Deposited 2023-02-10 Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 2–1341（1340 aa）
Not recorded PRF 7-DEAZA-7-AMINOMETHYL-GUANINE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION WAS CARRIED OUT IN A CHAMBER WITH THE TEMPERATURE SET TO 4 DEGREES CELSIUS.
Resolution 3.80 Å
8T00 Reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA: closed duplex DNA (rPTCc) Deposited 2023-05-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain I 2–1341（1340 aa）
Not recorded 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
8T0L E. coli Sw2/Snf2 ATPase RapA bound to both ADP-AlF3 and reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain I 2–1341（1340 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9DR1 E. coli RNA polymerase consensus volume with a bound fluoride riboswitch in the ligand-bound state Deposited 2024-09-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 2–1341（1340 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；5 mM Tris-HCl, pH 7.5, 100 mM KCl, 1 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9M7Y Cryo-EM structure of gp79-dependent RNAP promoter open complex Deposited 2025-03-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain A 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9M7Z Cryo-EM structure of gp79 bound RNAP core enzyme Deposited 2025-03-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.50 Å
9N07 Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1 state Deposited 2025-01-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 2–1341（1340 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9N11 Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1.5 state Deposited 2025-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 2–1341（1340 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.29 Å
9W3D Cryo-EM structure of E. coli RNA polymerase in complex with EP1 Deposited 2025-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9W3E Cryo-EM structure of E. coli RNA polymerase in complex with PP1 Deposited 2025-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9W3G Cryo-EM structure of E. coli RNA polymerase in complex with VP1 Deposited 2025-07-29 Different construct 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 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å

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 6
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 Other combination Heteromer Protein × 5 DNA 2 RNA 1 PDB declaration: octameric（8） Consistent with all polymer counts Chain J； UniProt 16–1373 Not recorded DNA (39-MER) × 1 DNA (31-MER) × 1 DNA-directed RNA polymerase subunit alpha × 2 （A0A5B9AW69） DNA-directed RNA polymerase subunit omega × 1 （A0A1X3IVJ5） RNA (48-MER) × 1 DNA-directed RNA polymerase subunit beta × 1 （C3SIA7） PRF 7-DEAZA-7-AMINOMETHYL-GUANINE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；Vitrification was carried out in a chamber with the temperature set to 4 C. Resolution 4.30 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 8G8Z Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6N4C EM structure of the DNA wrapping in bacterial open transcription initiation complex Deposited 2018-11-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain D 15–1376（1362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
Resolution 17.00 Å
8T00 Reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA: closed duplex DNA (rPTCc) Deposited 2023-05-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain J 16–1373（1358 aa）
Not recorded 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
8T0L E. coli Sw2/Snf2 ATPase RapA bound to both ADP-AlF3 and reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain J 16–1373（1358 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9DR1 E. coli RNA polymerase consensus volume with a bound fluoride riboswitch in the ligand-bound state Deposited 2024-09-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain J 16–1373（1358 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；5 mM Tris-HCl, pH 7.5, 100 mM KCl, 1 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9N11 Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1.5 state Deposited 2025-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain J 16–1373（1358 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.29 Å

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 7
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 8g8z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8g8z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8g8z
Deposition date deposition_date2023-02-20
Structure title titleCryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand
Keywords keywordsPolymerase, RNAP, riboswitch, aptamer, PreQ1, 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_guinier48.45 Å
Radius of gyration Rg (electron density) rg_electron47.95 Å
Forward intensity I(0) i02388600000.00
Molecular weight molecular_weight383630.0 kDa
Excluded volume excluded_volume470890 ų
Envelope volume envelope_volume683080 ų
Hydration-shell volume shell_volume112460 ų
Envelope diameter envelope_diameter163.4 Å
Shell Rg shell_rg56.24 Å
Envelope Rg envelope_rg47.65 Å
Shape Rg shape_rg47.96 Å
Total Rg total_rg48.19 Å
Total atoms total_atoms26822
Residues n_residues3266
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 dmax154.3 Å
Rg (real space) rg_real48.16 Å
Rg uncertainty (real space) rg_real_error0.77 Å
I(0) (real space) i0_real2.3890e+09
I(0) uncertainty (real space) i0_real_error3.9880e+07
Rg (reciprocal space) rg_reciprocal48.45 Å
I(0) (reciprocal space) i0_reciprocal2389000000.0000
Solution quality estimate total_estimate0.8779
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary60.8 Å
Skewness Skewness skewness0.209
Kurtosis Kurtosis kurtosis-0.365
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha353400000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.839
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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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8. Citations (1)

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9. Files and Curves (10)