7dy6

A refined cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA

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

Stringent starvation protein A

Escherichia coli (strain K12)

UniProt P0ACA3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 9 DNA 2 DNA (63-MER) × 1 DNA-directed RNA polymerase subunit alpha × 3 (A0A4S5AL01) DNA-directed RNA polymerase subunit beta × 1 (P0A8V2) ;DNA-directed RNA polymerase subunit beta' ; × 1 (P0A8T7) RNA polymerase sigma factor RpoD × 1 (P00579) DNA (63-MER) × 1 DNA-directed RNA polymerase subunit omega × 1 (A0A4S5AUM4) 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 SSPA_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain I; PDBConstruct 1–212; UniProt 1–212 Author chain J; PDBConstruct 1–212; UniProt 1–212

DNA-directed RNA polymerase subunit alpha

Escherichia coli (strain K12)

UniProt A0A4S5AL01

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 9 DNA 2 DNA (63-MER) × 1 Stringent starvation protein A × 2 (P0ACA3) DNA-directed RNA polymerase subunit beta × 1 (P0A8V2) ;DNA-directed RNA polymerase subunit beta' ; × 1 (P0A8T7) RNA polymerase sigma factor RpoD × 1 (P00579) DNA (63-MER) × 1 DNA-directed RNA polymerase subunit omega × 1 (A0A4S5AUM4) 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 A0A4S5AL01_ECOLI
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 1–329; UniProt 1–329 Author chain B; PDBConstruct 1–329; UniProt 1–329 Author chain K; PDBConstruct 1–329; UniProt 1–329

DNA-directed RNA polymerase subunit beta

Escherichia coli (strain K12)

UniProt P0A8V2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 9 DNA 2 DNA (63-MER) × 1 Stringent starvation protein A × 2 (P0ACA3) DNA-directed RNA polymerase subunit alpha × 3 (A0A4S5AL01) ;DNA-directed RNA polymerase subunit beta' ; × 1 (P0A8T7) RNA polymerase sigma factor RpoD × 1 (P00579) DNA (63-MER) × 1 DNA-directed RNA polymerase subunit omega × 1 (A0A4S5AUM4) 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_ECOLI
Isoform —
PDB entities 4
Chains and sequence ranges Author chain C; PDBConstruct 1–1342; UniProt 1–1342

;DNA-directed RNA polymerase subunit beta' ;

Escherichia coli (strain K12)

UniProt P0A8T7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 9 DNA 2 DNA (63-MER) × 1 Stringent starvation protein A × 2 (P0ACA3) DNA-directed RNA polymerase subunit alpha × 3 (A0A4S5AL01) DNA-directed RNA polymerase subunit beta × 1 (P0A8V2) RNA polymerase sigma factor RpoD × 1 (P00579) DNA (63-MER) × 1 DNA-directed RNA polymerase subunit omega × 1 (A0A4S5AUM4) 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 RPOC_ECOLI
Isoform —
PDB entities 5
Chains and sequence ranges Author chain D; PDBConstruct 1–1407; UniProt 1–1407

RNA polymerase sigma factor RpoD

Escherichia coli (strain K12)

UniProt P00579

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 9 DNA 2 DNA (63-MER) × 1 Stringent starvation protein A × 2 (P0ACA3) DNA-directed RNA polymerase subunit alpha × 3 (A0A4S5AL01) DNA-directed RNA polymerase subunit beta × 1 (P0A8V2) ;DNA-directed RNA polymerase subunit beta' ; × 1 (P0A8T7) DNA (63-MER) × 1 DNA-directed RNA polymerase subunit omega × 1 (A0A4S5AUM4) 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 RPOD_ECOLI
Isoform —
PDB entities 6
Chains and sequence ranges Author chain F; PDBConstruct 1–613; UniProt 1–613

DNA-directed RNA polymerase subunit omega

Escherichia coli (strain K12)

UniProt A0A4S5AUM4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 9 DNA 2 DNA (63-MER) × 1 Stringent starvation protein A × 2 (P0ACA3) DNA-directed RNA polymerase subunit alpha × 3 (A0A4S5AL01) DNA-directed RNA polymerase subunit beta × 1 (P0A8V2) ;DNA-directed RNA polymerase subunit beta' ; × 1 (P0A8T7) RNA polymerase sigma factor RpoD × 1 (P00579) DNA (63-MER) × 1 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 A0A4S5AUM4_ECOLI
Isoform —
PDB entities 8
Chains and sequence ranges Author chain E; PDBConstruct 1–91; UniProt 1–91

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_id7dy6
Deposition date deposition_date2021-01-20
Structure title titleA refined cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA
Keywords keywordsbacterial RNA polymerase, Complex, 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.

7dy6__assembly_1__model_1

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

Download this curve (.dat)

7dy6__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.

7dy6__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)55.74 Å
Rg (electron density)55.09 Å
Total Rg55.27 Å
Atom count35762
Residues4298
Excluded volume620490 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7dy6__assembly_1__model_1 undecameric (11) 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) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7dy6A01
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_id7dy6B01
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_id7dy6C01
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_id7dy6D01
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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7. Citations (1)