7mkn

Escherichia coli RNA polymerase and RapA elongation complex

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 (strain K12)

UniProt A0A4S5AL01

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 6 DNA 2 RNA 1 DNA-directed RNA polymerase subunit beta × 1 (A0A4S4NK82) ;DNA-directed RNA polymerase subunit beta' ; × 1 (A0A6D2WUT6) DNA-directed RNA polymerase subunit omega × 1 (P0A800) RNA polymerase-associated protein RapA × 1 (P60240) DNA (29-MER) × 1 RNA (20-MER) × 1 DNA (29-MER) × 1 MAGNESIUM ION × 1 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 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 1
Chains and sequence ranges Author chain A; PDBConstruct 1–237; UniProt 1–237 Author chain B; PDBConstruct 1–237; UniProt 1–237

DNA-directed RNA polymerase subunit beta

Escherichia coli (strain K12)

UniProt A0A4S4NK82

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 6 DNA 2 RNA 1 DNA-directed RNA polymerase subunit alpha × 2 (A0A4S5AL01) ;DNA-directed RNA polymerase subunit beta' ; × 1 (A0A6D2WUT6) DNA-directed RNA polymerase subunit omega × 1 (P0A800) RNA polymerase-associated protein RapA × 1 (P60240) DNA (29-MER) × 1 RNA (20-MER) × 1 DNA (29-MER) × 1 MAGNESIUM ION × 1 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A4S4NK82_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–1340; UniProt 3–1342

;DNA-directed RNA polymerase subunit beta' ;

Escherichia coli (strain K12)

UniProt A0A6D2WUT6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 6 DNA 2 RNA 1 DNA-directed RNA polymerase subunit alpha × 2 (A0A4S5AL01) DNA-directed RNA polymerase subunit beta × 1 (A0A4S4NK82) DNA-directed RNA polymerase subunit omega × 1 (P0A800) RNA polymerase-associated protein RapA × 1 (P60240) DNA (29-MER) × 1 RNA (20-MER) × 1 DNA (29-MER) × 1 MAGNESIUM ION × 1 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A6D2WUT6_ECOLI
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–1363; UniProt 14–1376

DNA-directed RNA polymerase subunit omega

Escherichia coli (strain K12)

UniProt P0A800

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 6 DNA 2 RNA 1 DNA-directed RNA polymerase subunit alpha × 2 (A0A4S5AL01) DNA-directed RNA polymerase subunit beta × 1 (A0A4S4NK82) ;DNA-directed RNA polymerase subunit beta' ; × 1 (A0A6D2WUT6) RNA polymerase-associated protein RapA × 1 (P60240) DNA (29-MER) × 1 RNA (20-MER) × 1 DNA (29-MER) × 1 MAGNESIUM ION × 1 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 Consistent with all polymers

Other States of the Same Protein in the Database

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

RNA polymerase-associated protein RapA

Escherichia coli (strain K12)

UniProt P60240

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 6 DNA 2 RNA 1 DNA-directed RNA polymerase subunit alpha × 2 (A0A4S5AL01) DNA-directed RNA polymerase subunit beta × 1 (A0A4S4NK82) ;DNA-directed RNA polymerase subunit beta' ; × 1 (A0A6D2WUT6) DNA-directed RNA polymerase subunit omega × 1 (P0A800) DNA (29-MER) × 1 RNA (20-MER) × 1 DNA (29-MER) × 1 MAGNESIUM ION × 1 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RAPA_ECOLI
Isoform —
PDB entities 5
Chains and sequence ranges Author chain L; PDBConstruct 1–968; UniProt 1–968

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_id7mkn
Deposition date deposition_date2021-04-26
Structure title titleEscherichia coli RNA polymerase and RapA elongation complex
Keywords keywordsRNAP recycling, RapA, Post-Termination Complex, PTC, TRANSCRIPTION, TRANSCRIPTION-DNA-RNA complex; TRANSCRIPTION/DNA/RNA
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.

7mkn__assembly_1__model_1

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

Download this curve (.dat)

7mkn__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.

7mkn__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)54.04 Å
Rg (electron density)54.01 Å
Total Rg54.02 Å
Atom count34084
Residues4239
Excluded volume601260 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7mkn__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 (11)

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id7mknA01
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_id7mknB01
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_id7mknD01
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_id7mknD02
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_id7mknE01
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
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7. Citations (1)