9q98

CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 1

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

Psp operon transcriptional activator

Escherichia coli K-12

UniProt P37344

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 12 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) RNA polymerase sigma-54 factor × 1 (A0A0N9UTC1) DNA Non-template strand (34-MER) × 1 DNA Template strand (34-MER) × 1 ADENOSINE-5'-DIPHOSPHATE × 5 ALUMINUM FLUORIDE × 5 MAGNESIUM ION × 5 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSPF_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain 1; PDBConstruct 1–259; UniProt 1–259 Author chain 2; PDBConstruct 1–259; UniProt 1–259 Author chain 3; PDBConstruct 1–259; UniProt 1–259 Author chain 4; PDBConstruct 1–259; UniProt 1–259 Author chain 5; PDBConstruct 1–259; UniProt 1–259 Author chain 6; PDBConstruct 1–259; UniProt 1–259

DNA-directed RNA polymerase subunit alpha

Escherichia coli K-12

UniProt P0A7Z4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 12 DNA 2 Psp operon transcriptional activator × 6 (P37344) 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 × 1 (A0A0N9UTC1) DNA Non-template strand (34-MER) × 1 DNA Template strand (34-MER) × 1 ADENOSINE-5'-DIPHOSPHATE × 5 ALUMINUM FLUORIDE × 5 MAGNESIUM ION × 5 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 2
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 K-12

UniProt P0A8V2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 12 DNA 2 Psp operon transcriptional activator × 6 (P37344) 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 × 1 (A0A0N9UTC1) DNA Non-template strand (34-MER) × 1 DNA Template strand (34-MER) × 1 ADENOSINE-5'-DIPHOSPHATE × 5 ALUMINUM FLUORIDE × 5 MAGNESIUM ION × 5 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 3
Chains and sequence ranges Author chain C; PDBConstruct 1–1342; UniProt 1–1342

;DNA-directed RNA polymerase subunit beta' ;

Escherichia coli K-12

UniProt P0A8T7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 12 DNA 2 Psp operon transcriptional activator × 6 (P37344) 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 × 1 (A0A0N9UTC1) DNA Non-template strand (34-MER) × 1 DNA Template strand (34-MER) × 1 ADENOSINE-5'-DIPHOSPHATE × 5 ALUMINUM FLUORIDE × 5 MAGNESIUM ION × 5 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 4
Chains and sequence ranges Author chain D; PDBConstruct 1–1407; UniProt 1–1407

DNA-directed RNA polymerase subunit omega

Escherichia coli K-12

UniProt P0A800

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 12 DNA 2 Psp operon transcriptional activator × 6 (P37344) 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 × 1 (A0A0N9UTC1) DNA Non-template strand (34-MER) × 1 DNA Template strand (34-MER) × 1 ADENOSINE-5'-DIPHOSPHATE × 5 ALUMINUM FLUORIDE × 5 MAGNESIUM ION × 5 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 5
Chains and sequence ranges Author chain E; PDBConstruct 1–91; UniProt 1–91

RNA polymerase sigma-54 factor

Klebsiella pneumoniae

UniProt A0A0N9UTC1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 12 DNA 2 Psp operon transcriptional activator × 6 (P37344) 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) DNA Non-template strand (34-MER) × 1 DNA Template strand (34-MER) × 1 ADENOSINE-5'-DIPHOSPHATE × 5 ALUMINUM FLUORIDE × 5 MAGNESIUM ION × 5 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A0N9UTC1_KLEPN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain M; PDBConstruct 1–477; UniProt 1–477

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_id9q98
Deposition date deposition_date2025-02-26
Structure title titleCryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 1
Keywords keywordssigma factor, transcription, complex, AAA+, DNA-binding protein; 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.

9q98__assembly_1__model_1

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

Download this curve (.dat)

9q98__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.

9q98__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)67.70 Å
Rg (electron density)68.17 Å
Total Rg68.02 Å
Atom count26958
Residues5222
Excluded volume431160 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9q98__assembly_1__model_1 tetradecameric (14) 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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7. Citations (1)