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5vo8

X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter

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

DNA-directed RNA polymerase subunit alpha

OrganismNot specified

UniProt Q5SHR6

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 （Q8RQE9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） DNA-directed RNA polymerase subunit omega × 1 （Q8RQE7） RNA polymerase sigma factor SigA × 1 （Q5SKW1） ;DNA (5'-D(P*GP*GP*TP*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*AP*AP*AP*A)-3') ; × 1 ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*CP*TP*GP*AP*TP*GP*CP*AP*CP*C)-3') ; × 1 ;RNA (5'-D(*(GTP))-R(P*GP*GP*GP*GP*GP*GP*G)-3') ; × 1 MAGNESIUM ION × 2 PYROPHOSPHATE 2- × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1zyr 1zyr 2a6e 2a6e 2a6h 2a6h 2cw0 2cw0 2o5i 2o5i 2o5j 2o5j

95 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RPOA_THET8
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–315； UniProt 1–315 Author chain B； PDBConstruct 1–315； UniProt 1–315

DNA-directed RNA polymerase subunit beta

OrganismNot specified

UniProt Q8RQE9

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 （Q5SHR6） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） DNA-directed RNA polymerase subunit omega × 1 （Q8RQE7） RNA polymerase sigma factor SigA × 1 （Q5SKW1） ;DNA (5'-D(P*GP*GP*TP*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*AP*AP*AP*A)-3') ; × 1 ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*CP*TP*GP*AP*TP*GP*CP*AP*CP*C)-3') ; × 1 ;RNA (5'-D(*(GTP))-R(P*GP*GP*GP*GP*GP*GP*G)-3') ; × 1 MAGNESIUM ION × 2 PYROPHOSPHATE 2- × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1smy 1smy 1zyr 1zyr 2a68 2a68 2a69 2a69 2a6e 2a6e 2a6h 2a6h

147 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RPOB_THET8
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–1119； UniProt 1–1119

;DNA-directed RNA polymerase subunit beta' ;

OrganismNot specified

UniProt Q8RQE8

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 （Q5SHR6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） DNA-directed RNA polymerase subunit omega × 1 （Q8RQE7） RNA polymerase sigma factor SigA × 1 （Q5SKW1） ;DNA (5'-D(P*GP*GP*TP*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*AP*AP*AP*A)-3') ; × 1 ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*CP*TP*GP*AP*TP*GP*CP*AP*CP*C)-3') ; × 1 ;RNA (5'-D(*(GTP))-R(P*GP*GP*GP*GP*GP*GP*G)-3') ; × 1 MAGNESIUM ION × 2 PYROPHOSPHATE 2- × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1smy 1smy 1zyr 1zyr 2a68 2a68 2a69 2a69 2a6e 2a6e 2a6h 2a6h

133 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RPOC_THET8
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–1524； UniProt 1–1524

DNA-directed RNA polymerase subunit omega

OrganismNot specified

UniProt Q8RQE7

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 （Q5SHR6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） RNA polymerase sigma factor SigA × 1 （Q5SKW1） ;DNA (5'-D(P*GP*GP*TP*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*AP*AP*AP*A)-3') ; × 1 ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*CP*TP*GP*AP*TP*GP*CP*AP*CP*C)-3') ; × 1 ;RNA (5'-D(*(GTP))-R(P*GP*GP*GP*GP*GP*GP*G)-3') ; × 1 MAGNESIUM ION × 2 PYROPHOSPHATE 2- × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1zyr 1zyr 2a6e 2a6e 2a6h 2a6h 2be5 2be5 2cw0 2cw0 2o5i 2o5i

113 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RPOZ_THET8
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E； PDBConstruct 1–99； UniProt 1–99

RNA polymerase sigma factor SigA

OrganismNot specified

UniProt Q5SKW1

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 （Q5SHR6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） DNA-directed RNA polymerase subunit omega × 1 （Q8RQE7） ;DNA (5'-D(P*GP*GP*TP*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*AP*AP*AP*A)-3') ; × 1 ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*CP*TP*GP*AP*TP*GP*CP*AP*CP*C)-3') ; × 1 ;RNA (5'-D(*(GTP))-R(P*GP*GP*GP*GP*GP*GP*G)-3') ; × 1 MAGNESIUM ION × 2 PYROPHOSPHATE 2- × 1 ZINC ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1zyr 1zyr 2a6e 2a6e 2a6h 2a6h 2be5 2be5 2cw0 2cw0 3dxj 3dxj

74 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q5SKW1_THET8
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F； PDBConstruct 1–423； UniProt 1–423

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_id5vo8
Deposition date deposition_date2017-05-02
Structure title titleX-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter
Keywords keywordsThermus thermophilus, RNA polymerase, reiterative transcription, holoenzyme, transcription-DNA-RNA complex; transcription/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.

5vo8__assembly_1__model_1

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

Download this curve (.dat)

5vo8__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.

5vo8__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）51.91 Å
Rg (electron density)52.83 Å
Total Rg52.79 Å
Atom count28534
Residues3526
Excluded volume506630 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5vo8__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_id5vo8A01
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_id5vo8A02
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_id5vo8B01
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_id5vo8B02
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_id5vo8C01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1110 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
Homologous superfamily homologous superfamily10 — RNA polymerase Rpb2, domain 2
Domain ID domain_id5vo8C02
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_id5vo8D01
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_id5vo8D02
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_id5vo8E00
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)