1ynn

Taq RNA polymerase-rifampicin complex

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

DNA-directed RNA polymerase alpha chain

OrganismNot specified

UniProt Q9KWU8

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 beta chain × 1 (Q9KWU7) ;DNA-directed RNA polymerase beta' chain ; × 2 (Q9KWU6) DNA-directed RNA polymerase omega chain × 1 (Q9EVV4) RIFAMPICIN × 1 ZINC ION × 2 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOA_THEAQ
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–314; UniProt 1–314 Author chain B; PDBConstruct 1–314; UniProt 1–314

DNA-directed RNA polymerase beta chain

OrganismNot specified

UniProt Q9KWU7

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 alpha chain × 2 (Q9KWU8) ;DNA-directed RNA polymerase beta' chain ; × 2 (Q9KWU6) DNA-directed RNA polymerase omega chain × 1 (Q9EVV4) RIFAMPICIN × 1 ZINC ION × 2 Consistent with protein count

Other States of the Same Protein in the Database

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

;DNA-directed RNA polymerase beta' chain ;

OrganismNot specified

UniProt Q9KWU6

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 alpha chain × 2 (Q9KWU8) DNA-directed RNA polymerase beta chain × 1 (Q9KWU7) DNA-directed RNA polymerase omega chain × 1 (Q9EVV4) RIFAMPICIN × 1 ZINC ION × 2 Consistent with protein count

Other States of the Same Protein in the Database

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

DNA-directed RNA polymerase omega chain

OrganismNot specified

UniProt Q9EVV4

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 alpha chain × 2 (Q9KWU8) DNA-directed RNA polymerase beta chain × 1 (Q9KWU7) ;DNA-directed RNA polymerase beta' chain ; × 2 (Q9KWU6) RIFAMPICIN × 1 ZINC ION × 2 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOZ_THEAQ
Isoform —
PDB entities 4
Chains and sequence ranges Author chain K; PDBConstruct 1–99; UniProt 0–98

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_id1ynn
Deposition date deposition_date2005-01-24
Structure title titleTaq RNA polymerase-rifampicin complex
Keywords keywordsTRANSFERASE, RNA polymerase, RIFAMPICIN; TRANSFERASE
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.

1ynn__assembly_1__model_1

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

Download this curve (.dat)

1ynn__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.

1ynn__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)53.82 Å
Rg (electron density)54.57 Å
Total Rg54.50 Å
Atom count24368
Residues3151
Excluded volume434520 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1ynn__assembly_1__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 (6)

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6. Fold Classification (SCOP + CATH) 25 domains

SCOP 2.08 (7 domains)

Domain ID domain_idd1ynna1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.74 — DCoH-like
Superfamily Superfamily superfamilyd.74.3 — RBP11-like subunits of RNA polymerase
Family Family familyd.74.3.1 — RNA polymerase alpha subunit dimerisation domain
Domain ID domain_idd1ynna2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.181 — Insert subdomain of RNA polymerase alpha subunit
Superfamily Superfamily superfamilyd.181.1 — Insert subdomain of RNA polymerase alpha subunit
Family Family familyd.181.1.1 — Insert subdomain of RNA polymerase alpha subunit
Domain ID domain_idd1ynnb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.74 — DCoH-like
Superfamily Superfamily superfamilyd.74.3 — RBP11-like subunits of RNA polymerase
Family Family familyd.74.3.1 — RNA polymerase alpha subunit dimerisation domain
Domain ID domain_idd1ynnb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.181 — Insert subdomain of RNA polymerase alpha subunit
Superfamily Superfamily superfamilyd.181.1 — Insert subdomain of RNA polymerase alpha subunit
Family Family familyd.181.1.1 — Insert subdomain of RNA polymerase alpha subunit
Domain ID domain_idd1ynnc1
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily Superfamily superfamilye.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Family Family familye.29.1.1 — RNA-polymerase beta
Domain ID domain_idd1ynnd1
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily Superfamily superfamilye.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Family Family familye.29.1.2 — RNA-polymerase beta-prime
Domain ID domain_idd1ynnk1
Class classa — All alpha proteins
Fold Fold folda.143 — RPB6/omega subunit-like
Superfamily Superfamily superfamilya.143.1 — RPB6/omega subunit-like
Family Family familya.143.1.1 — RNA polymerase omega subunit

CATH v4.4 (18 domains)

Domain ID domain_id1ynnA01
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_id1ynnA02
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_id1ynnB01
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_id1ynnB02
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_id1ynnC01
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_id1ynnC02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1100 — Rna Polymerase Beta Subunit; Chain: C,domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1ynnC03
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_id1ynnC04
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_id1ynnC05
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_id1ynnC06
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_id1ynnD03
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_id1ynnD04
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1ynnD05
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_id1ynnD06
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_id1ynnJ01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1790 — PTS-regulatory domain, PRD
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1ynnJ02
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_id1ynnJ03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily390 —
Domain ID domain_id1ynnK00
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 (2)