5ipl

SigmaS-transcription initiation complex with 4-nt nascent RNA

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

Escherichia coli

UniProt P0A7Z4

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 (P0A8V2) ;DNA-directed RNA polymerase subunit beta' ; × 1 (P0A8T7) DNA-directed RNA polymerase subunit omega × 1 (P0A800) RNA polymerase sigma factor RpoS × 1 (P13445) synthetic nontemplate strand DNA (50-MER) × 1 synthetic template strand DNA (50-MER) × 1 nascent RNA 4-mer × 1 DIPHOSPHATE × 1 ZINC ION × 2 MAGNESIUM ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOA_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 8–242; UniProt 1–235 Author chain B; PDBConstruct 8–242; UniProt 1–235

DNA-directed RNA polymerase subunit beta

Escherichia coli

UniProt P0A8V2

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 (P0A7Z4) ;DNA-directed RNA polymerase subunit beta' ; × 1 (P0A8T7) DNA-directed RNA polymerase subunit omega × 1 (P0A800) RNA polymerase sigma factor RpoS × 1 (P13445) synthetic nontemplate strand DNA (50-MER) × 1 synthetic template strand DNA (50-MER) × 1 nascent RNA 4-mer × 1 DIPHOSPHATE × 1 ZINC ION × 2 MAGNESIUM 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 2
Chains and sequence ranges Author chain C; PDBConstruct 1–1342; UniProt 1–1342

;DNA-directed RNA polymerase subunit beta' ;

Escherichia coli

UniProt P0A8T7

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 (P0A7Z4) DNA-directed RNA polymerase subunit beta × 1 (P0A8V2) DNA-directed RNA polymerase subunit omega × 1 (P0A800) RNA polymerase sigma factor RpoS × 1 (P13445) synthetic nontemplate strand DNA (50-MER) × 1 synthetic template strand DNA (50-MER) × 1 nascent RNA 4-mer × 1 DIPHOSPHATE × 1 ZINC ION × 2 MAGNESIUM 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 3
Chains and sequence ranges Author chain D; PDBConstruct 1–1407; UniProt 1–1407

DNA-directed RNA polymerase subunit omega

Escherichia coli

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 (P0A7Z4) DNA-directed RNA polymerase subunit beta × 1 (P0A8V2) ;DNA-directed RNA polymerase subunit beta' ; × 1 (P0A8T7) RNA polymerase sigma factor RpoS × 1 (P13445) synthetic nontemplate strand DNA (50-MER) × 1 synthetic template strand DNA (50-MER) × 1 nascent RNA 4-mer × 1 DIPHOSPHATE × 1 ZINC ION × 2 MAGNESIUM ION × 2 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 1–90; UniProt 2–91

RNA polymerase sigma factor RpoS

Escherichia coli

UniProt P13445

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 (P0A7Z4) DNA-directed RNA polymerase subunit beta × 1 (P0A8V2) ;DNA-directed RNA polymerase subunit beta' ; × 1 (P0A8T7) DNA-directed RNA polymerase subunit omega × 1 (P0A800) synthetic nontemplate strand DNA (50-MER) × 1 synthetic template strand DNA (50-MER) × 1 nascent RNA 4-mer × 1 DIPHOSPHATE × 1 ZINC ION × 2 MAGNESIUM ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOS_ECOLI
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F; PDBConstruct 1–330; UniProt 1–330

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_id5ipl
Deposition date deposition_date2016-03-09
Structure title titleSigmaS-transcription initiation complex with 4-nt nascent RNA
Keywords keywords;Transcription initiation, RNA polymerase, general stress sigma factor, pyrophosphate release, TRANSCRIPTION, TRANSFERASE-DNA-RNA complex ;; TRANSCRIPTION, TRANSFERASE/DNA/RNA
Experimental Method methodX-RAY DIFFRACTION
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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.

5ipl__assembly_1__model_1

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

Download this curve (.dat)

5ipl__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.

5ipl__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)48.07 Å
Rg (electron density)47.69 Å
Total Rg47.91 Å
Atom count27632
Residues3396
Excluded volume487030 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5ipl__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) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id5iplA01
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_id5iplA02
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_id5iplB01
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_id5iplB02
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_id5iplC01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology270 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
Homologous superfamily homologous superfamily10 — DNA-directed RNA polymerase, subunit 2, domain 6
Domain ID domain_id5iplC04
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology150 — Rna Polymerase Beta Subunit; Chain: C, domain 4
Homologous superfamily homologous superfamily10 — DNA-directed RNA polymerase, beta subunit, external 1 domain
Domain ID domain_id5iplC05
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_id5iplD01
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_id5iplE00
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)