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6bzo

Mtb RNAP Holo/RbpA/Fidaxomicin/upstream fork DNA

Method: ELECTRON MICROSCOPY Dmax: 181.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

Mycobacterium tuberculosis

UniProt A0A045J8T1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 7 DNA 2 PDB declaration: nonameric（9） Consistent with all polymer counts Chain A； UniProt 1–347 Chain B； UniProt 1–347 Not recorded DNA-directed RNA polymerase subunit beta × 1 （V9Z879） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A045J9E2） DNA-directed RNA polymerase subunit omega × 1 （A0A0T9N9K3） RNA polymerase sigma factor SigA × 1 （A0A045HD00） RNA polymerase-binding protein RbpA × 1 （A0A045IP01） DNA (32-MER) × 1 DNA (26-MER) × 1 FI8 Fidaxomicin × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.38 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6BZO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6C04 Mtb RNAP Holo/RbpA/double fork DNA -closed clamp Deposited 2017-12-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: undecameric
Chain A 1–347（347 aa）
Chain B 1–347（347 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
6C05 Mycobacterium tuberculosis RNAP Holo/RbpA in relaxed state Deposited 2017-12-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–347（347 aa）
Chain B 1–347（347 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å
6C06 Mycobacterium tuberculosis RNAP Holo/RbpA/Fidaxomicin Deposited 2017-12-27 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–347（347 aa）
Chain B 1–347（347 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 FI8 Fidaxomicin × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A045J8T1_MYCTX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–347； UniProt 1–347 Author chain B； PDBConstruct 1–347； UniProt 1–347

DNA-directed RNA polymerase subunit beta

Mycobacterium tuberculosis

UniProt V9Z879

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 7 DNA 2 PDB declaration: nonameric（9） Consistent with all polymer counts Chain C； UniProt 1–1172 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （A0A045J8T1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A045J9E2） DNA-directed RNA polymerase subunit omega × 1 （A0A0T9N9K3） RNA polymerase sigma factor SigA × 1 （A0A045HD00） RNA polymerase-binding protein RbpA × 1 （A0A045IP01） DNA (32-MER) × 1 DNA (26-MER) × 1 FI8 Fidaxomicin × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.38 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6BZO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6C04 Mtb RNAP Holo/RbpA/double fork DNA -closed clamp Deposited 2017-12-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: undecameric
Chain C 1–1172（1172 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
6C05 Mycobacterium tuberculosis RNAP Holo/RbpA in relaxed state Deposited 2017-12-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–1172（1172 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å
6C06 Mycobacterium tuberculosis RNAP Holo/RbpA/Fidaxomicin Deposited 2017-12-27 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–1172（1172 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 FI8 Fidaxomicin × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å
6EDT Mycobacterium tuberculosis RNAP open promoter complex with RbpA/CarD and AP3 promoter Deposited 2018-08-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–1134（1134 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EE8 Mycobacterium tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter Deposited 2018-08-13 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–1134（1134 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
6EEC Mycobacterium tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter captured by Corallopyronin Deposited 2018-08-13 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–1172（1172 aa）
Not recorded C0L methyl [(1E,5R)-5-{(3E)-3-[(2E,4E,8R,9E,12E)-1,8-dihydroxy-2,5,9-trimethyltetradeca-2,4,9,12-tetraen-1-ylidene]-2,4-dioxo-3,4-d ihydro-2H-pyran-6-yl}hex-1-en-1-yl]carbamate × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
6M7J Mycobacterium tuberculosis RNAP with RbpA/us fork and Corallopyronin Deposited 2018-08-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain C 1–1172（1172 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 C0L methyl [(1E,5R)-5-{(3E)-3-[(2E,4E,8R,9E,12E)-1,8-dihydroxy-2,5,9-trimethyltetradeca-2,4,9,12-tetraen-1-ylidene]-2,4-dioxo-3,4-d ihydro-2H-pyran-6-yl}hex-1-en-1-yl]carbamate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6VVX Mycobacterium tuberculosis WT RNAP transcription initiation intermediate structure with Sorangicin Deposited 2020-02-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–1172（1172 aa）
Not recorded SRN SORANGICIN A × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
6VVY Mycobacterium tuberculosis WT RNAP transcription open promoter complex with Sorangicin Deposited 2020-02-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–1172（1172 aa）
Not recorded SRN SORANGICIN A × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
6VVZ Mycobacterium tuberculosis RNAP S456L mutant transcription initiation intermediate structure with Sorangicin Deposited 2020-02-18 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–1172（1172 aa）
Mutation：S456L SRN SORANGICIN A × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å
6VW0 Mycobacterium tuberculosis RNAP S456L mutant open promoter complex Deposited 2020-02-18 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–1172（1172 aa）
Mutation：S456L ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name V9Z879_MYCTX
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–1172； UniProt 1–1172

;DNA-directed RNA polymerase subunit beta' ;

Mycobacterium tuberculosis

UniProt A0A045J9E2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 7 DNA 2 PDB declaration: nonameric（9） Consistent with all polymer counts Chain D； UniProt 1–1316 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （A0A045J8T1） DNA-directed RNA polymerase subunit beta × 1 （V9Z879） DNA-directed RNA polymerase subunit omega × 1 （A0A0T9N9K3） RNA polymerase sigma factor SigA × 1 （A0A045HD00） RNA polymerase-binding protein RbpA × 1 （A0A045IP01） DNA (32-MER) × 1 DNA (26-MER) × 1 FI8 Fidaxomicin × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.38 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6BZO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6C04 Mtb RNAP Holo/RbpA/double fork DNA -closed clamp Deposited 2017-12-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: undecameric
Chain D 1–1316（1316 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
6C05 Mycobacterium tuberculosis RNAP Holo/RbpA in relaxed state Deposited 2017-12-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–1316（1316 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å
6C06 Mycobacterium tuberculosis RNAP Holo/RbpA/Fidaxomicin Deposited 2017-12-27 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–1316（1316 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 FI8 Fidaxomicin × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å
6TYF Crystal structure of MTB sigma L transcription initiation complex with 6 nt long RNA primer Deposited 2019-08-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1316（1316 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM sodium citrate tribasic dihydrate, pH 5.6, 200 mM sodium acetate, and 10% PEG4000
Resolution 3.80 Å R-free 0.300
6TYG Crystal structure of MTB sigma L transcription initiation complex with 9 nt long RNA primer Deposited 2019-08-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1316（1316 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM sodium citrate tribasic dihydrate, pH 5.6, 200 mM sodium acetate, and 10% PEG4000
Resolution 3.50 Å R-free 0.293
7KIF Mycobacterium tuberculosis WT RNAP transcription open promoter complex with WhiB7 transcription factor Deposited 2020-10-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–1316（1316 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
7KIM Mycobacterium tuberculosis WT RNAP transcription closed promoter complex with WhiB7 transcription factor Deposited 2020-10-23 Different oligomeric state Different ligand/ion Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–1316（1316 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
7KIN Mycobacterium tuberculosis WT RNAP transcription open promoter complex with WhiB7 promoter Deposited 2020-10-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–1316（1316 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.74 Å
7RWI Mycobacterium tuberculosis RNA polymerase sigma L holoenzyme open promoter complex containing TNP-2198 Deposited 2021-08-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain D 1–1316（1316 aa）
Not recorded 7US (3aM,9S,10bP,14S,15R,16S,17R,18R,19R,20S,21S,25R)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM sodium citrate tribasic dihydrate, pH 5.6, 200 mM sodium acetate, 10% PEG4000
Resolution 3.70 Å R-free 0.245
7U22 Mycobacterium tuberculosis RNA polymerase sigma A holoenzyme open promoter complex containing UMN-7 Deposited 2022-02-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain D 1–1316（1316 aa）
Not recorded KYO (9S,14S,15R,16S,17R,18R,19R,20S,21S,25R)-5,6,18,20-tetrahydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-(2-methylpropyl)-10,26-dioxo-1,3,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl benzoate × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；296 K；20 mM Tris-HCl, pH 8.2, 200 mM potassium chloride, 20 mM magnesium chloride, 7% (m/v) PEG-3350
Resolution 3.87 Å R-free 0.278
8E74 Mycobacterium tuberculosis RNAP paused elongation complex with NusG transcription factor Deposited 2022-08-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1316（1316 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
8E79 Mycobacterium tuberculosis RNAP paused elongation complex with Escherichia coli NusG transcription factor Deposited 2022-08-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1316（1316 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.71 Å
8E82 Mycobacterium tuberculosis RNAP elongation complex with NusG transcription factor Deposited 2022-08-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1316（1316 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
8E8M Mycobacterium tuberculosis RNAP paused elongation complex Deposited 2022-08-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain D 1–1316（1316 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8E95 Mycobacterium tuberculosis RNAP elongation complex Deposited 2022-08-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain D 1–1316（1316 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A045J9E2_MYCTX
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–1316； UniProt 1–1316

DNA-directed RNA polymerase subunit omega

Mycobacterium tuberculosis

UniProt A0A0T9N9K3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 7 DNA 2 PDB declaration: nonameric（9） Consistent with all polymer counts Chain E； UniProt 41–149 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （A0A045J8T1） DNA-directed RNA polymerase subunit beta × 1 （V9Z879） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A045J9E2） RNA polymerase sigma factor SigA × 1 （A0A045HD00） RNA polymerase-binding protein RbpA × 1 （A0A045IP01） DNA (32-MER) × 1 DNA (26-MER) × 1 FI8 Fidaxomicin × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.38 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6BZO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6C04 Mtb RNAP Holo/RbpA/double fork DNA -closed clamp Deposited 2017-12-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: undecameric
Chain E 41–149（109 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
6C05 Mycobacterium tuberculosis RNAP Holo/RbpA in relaxed state Deposited 2017-12-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 41–149（109 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å
6C06 Mycobacterium tuberculosis RNAP Holo/RbpA/Fidaxomicin Deposited 2017-12-27 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 41–149（109 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 FI8 Fidaxomicin × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å
6EDT Mycobacterium tuberculosis RNAP open promoter complex with RbpA/CarD and AP3 promoter Deposited 2018-08-10 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 41–149（109 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EE8 Mycobacterium tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter Deposited 2018-08-13 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 41–149（109 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
6EEC Mycobacterium tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter captured by Corallopyronin Deposited 2018-08-13 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 41–149（109 aa）
Not recorded C0L methyl [(1E,5R)-5-{(3E)-3-[(2E,4E,8R,9E,12E)-1,8-dihydroxy-2,5,9-trimethyltetradeca-2,4,9,12-tetraen-1-ylidene]-2,4-dioxo-3,4-d ihydro-2H-pyran-6-yl}hex-1-en-1-yl]carbamate × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
6M7J Mycobacterium tuberculosis RNAP with RbpA/us fork and Corallopyronin Deposited 2018-08-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain E 41–149（109 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 C0L methyl [(1E,5R)-5-{(3E)-3-[(2E,4E,8R,9E,12E)-1,8-dihydroxy-2,5,9-trimethyltetradeca-2,4,9,12-tetraen-1-ylidene]-2,4-dioxo-3,4-d ihydro-2H-pyran-6-yl}hex-1-en-1-yl]carbamate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6VVX Mycobacterium tuberculosis WT RNAP transcription initiation intermediate structure with Sorangicin Deposited 2020-02-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 41–149（109 aa）
Not recorded SRN SORANGICIN A × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
6VVY Mycobacterium tuberculosis WT RNAP transcription open promoter complex with Sorangicin Deposited 2020-02-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 41–149（109 aa）
Not recorded SRN SORANGICIN A × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
6VVZ Mycobacterium tuberculosis RNAP S456L mutant transcription initiation intermediate structure with Sorangicin Deposited 2020-02-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 41–149（109 aa）
Not recorded SRN SORANGICIN A × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å
6VW0 Mycobacterium tuberculosis RNAP S456L mutant open promoter complex Deposited 2020-02-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 41–149（109 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
7KIF Mycobacterium tuberculosis WT RNAP transcription open promoter complex with WhiB7 transcription factor Deposited 2020-10-23 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain E 40–149（110 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
7KIM Mycobacterium tuberculosis WT RNAP transcription closed promoter complex with WhiB7 transcription factor Deposited 2020-10-23 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain E 40–149（110 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
7KIN Mycobacterium tuberculosis WT RNAP transcription open promoter complex with WhiB7 promoter Deposited 2020-10-23 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 40–149（110 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.74 Å
8E74 Mycobacterium tuberculosis RNAP paused elongation complex with NusG transcription factor Deposited 2022-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain E 40–149（110 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
8E79 Mycobacterium tuberculosis RNAP paused elongation complex with Escherichia coli NusG transcription factor Deposited 2022-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain E 40–149（110 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.71 Å
8E82 Mycobacterium tuberculosis RNAP elongation complex with NusG transcription factor Deposited 2022-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain E 40–149（110 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
8E8M Mycobacterium tuberculosis RNAP paused elongation complex Deposited 2022-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain E 40–149（110 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8E95 Mycobacterium tuberculosis RNAP elongation complex Deposited 2022-08-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain E 40–149（110 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A0T9N9K3_MYCTX
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E； PDBConstruct 2–110； UniProt 41–149

RNA polymerase sigma factor SigA

Mycobacterium tuberculosis

UniProt A0A045HD00

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 7 DNA 2 PDB declaration: nonameric（9） Consistent with all polymer counts Chain F； UniProt 1–528 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （A0A045J8T1） DNA-directed RNA polymerase subunit beta × 1 （V9Z879） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A045J9E2） DNA-directed RNA polymerase subunit omega × 1 （A0A0T9N9K3） RNA polymerase-binding protein RbpA × 1 （A0A045IP01） DNA (32-MER) × 1 DNA (26-MER) × 1 FI8 Fidaxomicin × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.38 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6BZO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6C04 Mtb RNAP Holo/RbpA/double fork DNA -closed clamp Deposited 2017-12-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: undecameric
Chain F 1–528（528 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
6C05 Mycobacterium tuberculosis RNAP Holo/RbpA in relaxed state Deposited 2017-12-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–528（528 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å
6C06 Mycobacterium tuberculosis RNAP Holo/RbpA/Fidaxomicin Deposited 2017-12-27 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–528（528 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 FI8 Fidaxomicin × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å
7U22 Mycobacterium tuberculosis RNA polymerase sigma A holoenzyme open promoter complex containing UMN-7 Deposited 2022-02-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain F 1–528（528 aa）
Not recorded KYO (9S,14S,15R,16S,17R,18R,19R,20S,21S,25R)-5,6,18,20-tetrahydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-(2-methylpropyl)-10,26-dioxo-1,3,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl benzoate × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；296 K；20 mM Tris-HCl, pH 8.2, 200 mM potassium chloride, 20 mM magnesium chloride, 7% (m/v) PEG-3350
Resolution 3.87 Å R-free 0.278
9JI2 Cryo-EM structure of Mycobacterium tuberculosis transcription activation complex with unphosphated PhoP Deposited 2024-09-11 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain F 1–528（528 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
9JI3 Cryo-EM structure of Mycobacterium tuberculosis transcription activation complex with two PhoP molecules Deposited 2024-09-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 1–528（528 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
9JI4 Cryo-EM structure of Mycobacterium tuberculosis transcription activation complex with four PhoP molecules Deposited 2024-09-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain F 1–528（528 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
9JI5 Cryo-EM structure of Mycobacterium tuberculosis transcription activation complex with six PhoP molecules Deposited 2024-09-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain F 1–528（528 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A045HD00_MYCTX
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F； PDBConstruct 4–531； UniProt 1–528

RNA polymerase-binding protein RbpA

Mycobacterium tuberculosis

UniProt A0A045IP01

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 7 DNA 2 PDB declaration: nonameric（9） Consistent with all polymer counts Chain J； UniProt 1–111 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （A0A045J8T1） DNA-directed RNA polymerase subunit beta × 1 （V9Z879） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A045J9E2） DNA-directed RNA polymerase subunit omega × 1 （A0A0T9N9K3） RNA polymerase sigma factor SigA × 1 （A0A045HD00） DNA (32-MER) × 1 DNA (26-MER) × 1 FI8 Fidaxomicin × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.38 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6BZO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6C04 Mtb RNAP Holo/RbpA/double fork DNA -closed clamp Deposited 2017-12-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: undecameric
Chain J 1–111（111 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
6C05 Mycobacterium tuberculosis RNAP Holo/RbpA in relaxed state Deposited 2017-12-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain J 1–111（111 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å
6C06 Mycobacterium tuberculosis RNAP Holo/RbpA/Fidaxomicin Deposited 2017-12-27 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain J 1–111（111 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 FI8 Fidaxomicin × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A045IP01_MYCTX
Isoform —
PDB entities 6
Chains and sequence ranges Author chain J； PDBConstruct 1–111； UniProt 1–111

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6bzo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6bzo
Download Download
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6bzo
Deposition date deposition_date2017-12-25
Structure title titleMtb RNAP Holo/RbpA/Fidaxomicin/upstream fork DNA
Keywords keywordsRNA Polymerase, Antibiotic, Inhibitor, TRANSCRIPTION, transcription-dna-antibiotic complex; transcription/dna/antibiotic
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier52.15 Å
Radius of gyration Rg (electron density) rg_electron51.19 Å
Forward intensity I(0) i02341020000.00
Molecular weight molecular_weight388690.0 kDa
Excluded volume excluded_volume480720 ų
Envelope volume envelope_volume720950 ų
Hydration-shell volume shell_volume114250 ų
Envelope diameter envelope_diameter197.7 Å
Shell Rg shell_rg57.38 Å
Envelope Rg envelope_rg50.57 Å
Shape Rg shape_rg51.17 Å
Total Rg total_rg51.42 Å
Total atoms total_atoms27330
Residues n_residues3410
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax181.3 Å
Rg (real space) rg_real52.05 Å
Rg uncertainty (real space) rg_real_error1.58 Å
I(0) (real space) i0_real2.3410e+09
I(0) uncertainty (real space) i0_real_error4.6330e+07
Rg (reciprocal space) rg_reciprocal52.23 Å
I(0) (reciprocal space) i0_reciprocal2342000000.0000
Solution quality estimate total_estimate0.6247
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary66.5 Å
Skewness Skewness skewness0.333
Kurtosis Kurtosis kurtosis-0.080
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha290200000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.736; Stabil: 1.000; Sysdev: 0.007; Positv: 1.000; Valcen: 0.970; Smooth: 0.918
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (12)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id6bzoA01
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_id6bzoA02
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_id6bzoB01
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_id6bzoB02
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_id6bzoD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily100 — RNA polymerase Rpb1, domain 3
Domain ID domain_id6bzoD02
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
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8. Citations (1)

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9. Files and Curves (10)