6kql

Thermus thermophilus initial transcription complex comprising sigma A and 5'-triphosphate RNA of 4 nt

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(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3') ; × 1 ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*G*)-3') ; × 1 ;RNA (5'-R(*(UTP))-R(P*CP*GP*A)-3') ; × 1 ZINC ION × 2 MAGNESIUM ION × 4 water × 8 Consistent with all polymers

Other States of the Same Protein in the Database

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(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3') ; × 1 ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*G*)-3') ; × 1 ;RNA (5'-R(*(UTP))-R(P*CP*GP*A)-3') ; × 1 ZINC ION × 2 MAGNESIUM ION × 4 water × 8 Consistent with all polymers

Other States of the Same Protein in the Database

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(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3') ; × 1 ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*G*)-3') ; × 1 ;RNA (5'-R(*(UTP))-R(P*CP*GP*A)-3') ; × 1 ZINC ION × 2 MAGNESIUM ION × 4 water × 8 Consistent with all polymers

Other States of the Same Protein in the Database

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(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3') ; × 1 ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*G*)-3') ; × 1 ;RNA (5'-R(*(UTP))-R(P*CP*GP*A)-3') ; × 1 ZINC ION × 2 MAGNESIUM ION × 4 water × 8 Consistent with all polymers

Other States of the Same Protein in the Database

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

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3') ; × 1 ;DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*G*)-3') ; × 1 ;RNA (5'-R(*(UTP))-R(P*CP*GP*A)-3') ; × 1 ZINC ION × 2 MAGNESIUM ION × 4 water × 8 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name Q5SKW1_THET8
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F; PDBConstruct 21–443; 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_id6kql
Deposition date deposition_date2019-08-18
Structure title titleThermus thermophilus initial transcription complex comprising sigma A and 5'-triphosphate RNA of 4 nt
Keywords keywords;Thermus thermophilus, RNA polymerase, transcription initiation complex, 5'-triphosphate, 4nt RNA, TRANSCRIPTION ;; TRANSCRIPTION
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.

6kql__assembly_1__model_1

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

Download this curve (.dat)

6kql__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.

6kql__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)52.77 Å
Total Rg52.75 Å
Atom count28601
Residues3540
Excluded volume508230 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6kql__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_id6kqlA01
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_id6kqlA02
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_id6kqlB01
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_id6kqlB02
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_id6kqlC01
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_id6kqlC02
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_id6kqlD01
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_id6kqlD02
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_id6kqlE00
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)