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4yfn

Escherichia coli RNA polymerase in complex with squaramide compound 14 (N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide)

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 O139:H28 (strain E24377A / ETEC)

UniProt A7ZSI4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） MAGNESIUM ION × 1 ZINC ION × 2 N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） MAGNESIUM ION × 1 ZINC ION × 2 N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4xsx 4xsx 4xsy 4xsy 4xsz 4xsz 4yfk 4yfk 4yfn 4yfn 4yfx 4yfx

21 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RPOA_ECO24
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 Author chain G； PDBConstruct 1–329； UniProt 1–329 Author chain H； PDBConstruct 1–329； UniProt 1–329

DNA-directed RNA polymerase subunit beta

Escherichia coli O139:H28 (strain E24377A / ETEC)

UniProt A7ZUK1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） MAGNESIUM ION × 1 ZINC ION × 2 N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） MAGNESIUM ION × 1 ZINC ION × 2 N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4xsx 4xsx 4xsy 4xsy 4xsz 4xsz 4yfk 4yfk 4yfn 4yfn 4yfx 4yfx

22 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RPOB_ECO24
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–1342； UniProt 1–1342 Author chain I； PDBConstruct 1–1342； UniProt 1–1342

;DNA-directed RNA polymerase subunit beta' ;

Escherichia coli O139:H28 (strain E24377A / ETEC)

UniProt A7ZUK2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） MAGNESIUM ION × 1 ZINC ION × 2 N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） MAGNESIUM ION × 1 ZINC ION × 2 N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4xsx 4xsx 4xsy 4xsy 4xsz 4xsz 4yfk 4yfk 4yfn 4yfn 4yfx 4yfx

25 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RPOC_ECO24
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–1407； UniProt 1–1407 Author chain J； PDBConstruct 1–1407； UniProt 1–1407

DNA-directed RNA polymerase subunit omega

Escherichia coli O139:H28 (strain E24377A / ETEC)

UniProt A7ZTK1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） RNA polymerase sigma factor RpoD × 1 （P00579） MAGNESIUM ION × 1 ZINC ION × 2 N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） RNA polymerase sigma factor RpoD × 1 （P00579） MAGNESIUM ION × 1 ZINC ION × 2 N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4yfk 4yfk 4yfn 4yfn 4yfx 4yfx 4yln 4yln 4yln 4ylo 4ylo 4ylo

16 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RPOZ_ECO24
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E； PDBConstruct 1–91； UniProt 1–91 Author chain K； PDBConstruct 1–91； UniProt 1–91

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 heterocomplex Heteromer Protein 6 DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） MAGNESIUM ION × 1 ZINC ION × 2 N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） MAGNESIUM ION × 1 ZINC ION × 2 N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1sig

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1tlh 2p7v 2p7v 3iyd 3t72 3t72 4jk1 4jk1 4jk2 4jk2 4jkr 4jkr

132 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RPOD_ECOLI
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F； PDBConstruct 1–613； UniProt 1–613 Author chain L； PDBConstruct 1–613； UniProt 1–613

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_id4yfn
Deposition date deposition_date2015-02-25
Structure title titleEscherichia coli RNA polymerase in complex with squaramide compound 14 (N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide)
Keywords keywordsswitch region, squaramide, transcription-transcription inhibitor complex; transcription/transcription inhibitor
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.

4yfn__assembly_1__model_1

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

Download this curve (.dat)

4yfn__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.

4yfn__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）52.88 Å
Rg (electron density)52.66 Å
Total Rg52.84 Å
Atom count28195
Residues3584
Excluded volume502370 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4yfn__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4yfn__assembly_2__model_1 hexameric （6） 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 (8)

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6. Fold Classification (SCOP + CATH) 27 domains

CATH v4.4 (27 domains)

Domain ID domain_id4yfnA01
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_id4yfnA02
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_id4yfnB01
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_id4yfnB02
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_id4yfnB03
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_id4yfnC01
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_id4yfnC04
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_id4yfnC05
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_id4yfnC06
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_id4yfnC07
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily1670 —
Domain ID domain_id4yfnD01
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_id4yfnE00
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
Domain ID domain_id4yfnF01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology601 — RNA Polymerase Primary Sigma Factor
Homologous superfamily homologous superfamily10 — RNA Polymerase Primary Sigma Factor
Domain ID domain_id4yfnF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id4yfnF03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id4yfnG01
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_id4yfnG02
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_id4yfnH01
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_id4yfnH02
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_id4yfnI01
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_id4yfnI04
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_id4yfnI05
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_id4yfnJ01
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_id4yfnK00
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
Domain ID domain_id4yfnL01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology601 — RNA Polymerase Primary Sigma Factor
Homologous superfamily homologous superfamily10 — RNA Polymerase Primary Sigma Factor
Domain ID domain_id4yfnL02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id4yfnL03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
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7. Citations (1)