6oul

Cryo-EM structure of Escherichia coli RNAP polymerase bound to rpsTP2 promoter DNA

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

Escherichia coli

UniProt A0A073G207

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 7 DNA 2 DNA-directed RNA polymerase subunit beta × 1 (P0A8V4) ;DNA-directed RNA polymerase subunit beta' ; × 1 (U9YPW3) DNA-directed RNA polymerase subunit omega × 1 (P0A802) RNA polymerase sigma factor RpoD × 1 (Q0P6L9) Non-template strand of rpsTP2 DNA promoter × 1 Template strand of rpsTP2 DNA promoter × 1 CHAPSO × 3 MAGNESIUM ION × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A073G207_ECOLX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain G; PDBConstruct 1–329; UniProt 1–329 Author chain H; PDBConstruct 1–329; UniProt 1–329 Author chain R; PDBConstruct 1–329; UniProt 1–329

DNA-directed RNA polymerase subunit beta

Escherichia coli

UniProt P0A8V4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 7 DNA 2 DNA-directed RNA polymerase subunit alpha × 3 (A0A073G207) ;DNA-directed RNA polymerase subunit beta' ; × 1 (U9YPW3) DNA-directed RNA polymerase subunit omega × 1 (P0A802) RNA polymerase sigma factor RpoD × 1 (Q0P6L9) Non-template strand of rpsTP2 DNA promoter × 1 Template strand of rpsTP2 DNA promoter × 1 CHAPSO × 3 MAGNESIUM ION × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOB_ECO57
Isoform —
PDB entities 2
Chains and sequence ranges Author chain I; PDBConstruct 1–1342; UniProt 1–1342

;DNA-directed RNA polymerase subunit beta' ;

Escherichia coli

UniProt U9YPW3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 7 DNA 2 DNA-directed RNA polymerase subunit alpha × 3 (A0A073G207) DNA-directed RNA polymerase subunit beta × 1 (P0A8V4) DNA-directed RNA polymerase subunit omega × 1 (P0A802) RNA polymerase sigma factor RpoD × 1 (Q0P6L9) Non-template strand of rpsTP2 DNA promoter × 1 Template strand of rpsTP2 DNA promoter × 1 CHAPSO × 3 MAGNESIUM ION × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name U9YPW3_ECOLX
Isoform —
PDB entities 3
Chains and sequence ranges Author chain J; PDBConstruct 2–1407; UniProt 2–1407

DNA-directed RNA polymerase subunit omega

Escherichia coli

UniProt P0A802

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 7 DNA 2 DNA-directed RNA polymerase subunit alpha × 3 (A0A073G207) DNA-directed RNA polymerase subunit beta × 1 (P0A8V4) ;DNA-directed RNA polymerase subunit beta' ; × 1 (U9YPW3) RNA polymerase sigma factor RpoD × 1 (Q0P6L9) Non-template strand of rpsTP2 DNA promoter × 1 Template strand of rpsTP2 DNA promoter × 1 CHAPSO × 3 MAGNESIUM ION × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOZ_ECO57
Isoform —
PDB entities 4
Chains and sequence ranges Author chain K; PDBConstruct 1–91; UniProt 1–91

RNA polymerase sigma factor RpoD

Escherichia coli

UniProt Q0P6L9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 7 DNA 2 DNA-directed RNA polymerase subunit alpha × 3 (A0A073G207) DNA-directed RNA polymerase subunit beta × 1 (P0A8V4) ;DNA-directed RNA polymerase subunit beta' ; × 1 (U9YPW3) DNA-directed RNA polymerase subunit omega × 1 (P0A802) Non-template strand of rpsTP2 DNA promoter × 1 Template strand of rpsTP2 DNA promoter × 1 CHAPSO × 3 MAGNESIUM ION × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name Q0P6L9_ECOLX
Isoform —
PDB entities 5
Chains and sequence ranges Author chain L; PDBConstruct 4–616; UniProt 1–613

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id6oul
Deposition date deposition_date2019-05-04
Structure title titleCryo-EM structure of Escherichia coli RNAP polymerase bound to rpsTP2 promoter DNA
Keywords keywordsprotein-DNA complex, transcription initiation, RNA polyermase, DNA promoter melting, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodELECTRON MICROSCOPY
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6oul__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6oul__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6oul__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)53.71 Å
Rg (electron density)52.80 Å
Total Rg53.06 Å
Atom count32044
Residues3868
Excluded volume561840 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6oul__assembly_1__model_1 nonameric (9) Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (10)

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6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id6oulG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily10 — RNA polymerase, RBP11-like subunit
Domain ID domain_id6oulG02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily12 — DNA-directed RNA polymerase, insert domain
Domain ID domain_id6oulH01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily10 — RNA polymerase, RBP11-like subunit
Domain ID domain_id6oulH02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily12 — DNA-directed RNA polymerase, insert domain
Domain ID domain_id6oulI01
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_id6oulJ01
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_id6oulJ02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain
Domain ID domain_id6oulK00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology940 — Eukaryotic RPB6 RNA polymerase subunit
Homologous superfamily homologous superfamily10 — RNA polymerase subunit, RPB6/omega
Domain ID domain_id6oulR00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
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7. Citations (1)