6gh5

Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme transcription open 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 P0A7Z4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 6 DNA 2 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-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor ; × 1 (A0A0J4U551) nifH promoter template DNA × 1 nifH promoter non-template DNA × 1 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 1–329; UniProt 1–329 Author chain B; 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 6 DNA 2 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-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor ; × 1 (A0A0J4U551) nifH promoter template DNA × 1 nifH promoter non-template DNA × 1 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 (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 6 DNA 2 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-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor ; × 1 (A0A0J4U551) nifH promoter template DNA × 1 nifH promoter non-template DNA × 1 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 (strain K12)

UniProt P0A800

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 6 DNA 2 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-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor ; × 1 (A0A0J4U551) nifH promoter template DNA × 1 nifH promoter non-template DNA × 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 sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor ;

Klebsiella pneumoniae

UniProt A0A0J4U551

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 6 DNA 2 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) nifH promoter template DNA × 1 nifH promoter non-template DNA × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A0J4U551_KLEPN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain M; PDBConstruct 21–277; UniProt 1–257 Author chain M; PDBConstruct 314–417; UniProt 294–397 Author chain M; PDBConstruct 434–497; UniProt 414–477

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_id6gh5
Deposition date deposition_date2018-05-04
Structure title titleCryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme transcription open complex
Keywords keywordstranscription initiation, DNA opening, transcription bubble, open 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.

6gh5__assembly_1__model_1

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

Download this curve (.dat)

6gh5__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.

6gh5__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)50.46 Å
Rg (electron density)49.60 Å
Total Rg49.81 Å
Atom count28316
Residues3735
Excluded volume495360 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6gh5__assembly_1__model_1 octameric (8) 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 (7)

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6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id6gh5A01
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_id6gh5A02
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_id6gh5A03
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
Domain ID domain_id6gh5B01
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_id6gh5B02
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_id6gh5D01
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_id6gh5E00
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)