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1iw7

Crystal structure of the RNA polymerase holoenzyme from Thermus thermophilus at 2.6A resolution

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

RNA polymerase alpha subunit

OrganismNot specified

UniProt Q9Z9H6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 RNA polymerase beta subunit × 1 RNA polymerase beta subunit × 1 RNA polymerase omega subunit × 1 RNA polymerase sigma-70 subunit × 1 MAGNESIUM ION × 260 LEAD (II) ION × 2 water × 6 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 RNA polymerase beta subunit × 1 RNA polymerase beta subunit × 1 RNA polymerase omega subunit × 1 RNA polymerase sigma-70 subunit × 1 MAGNESIUM ION × 225 LEAD (II) ION × 2 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1doq

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1iw7 1iw7 1smy 1smy 2a68 2a68 2a69 2a69 2be5 2be5 2ppb 2ppb

38 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RPOA_THETH
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 Author chain K； PDBConstruct 1–315； UniProt 1–315 Author chain L； PDBConstruct 1–315； UniProt 1–315

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_id1iw7
Deposition date deposition_date2002-04-22
Structure title titleCrystal structure of the RNA polymerase holoenzyme from Thermus thermophilus at 2.6A resolution
Keywords keywordsRNA polymerase holoenzyme, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, TRANSFERASE; 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.

1iw7__assembly_1__model_1

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

Download this curve (.dat)

1iw7__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.

1iw7__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）50.50 Å
Rg (electron density)50.15 Å
Total Rg50.42 Å
Atom count27044
Residues3409
Excluded volume483900 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1iw7__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1iw7__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) 61 domains

SCOP 2.08 (20 domains)

Domain ID domain_idd1iw7a1
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_idd1iw7a2
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_idd1iw7b1
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_idd1iw7b2
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_idd1iw7c_
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_idd1iw7d_
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_idd1iw7e_
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
Domain ID domain_idd1iw7f1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.13 — Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family Family familya.4.13.1 — Sigma3 domain
Domain ID domain_idd1iw7f2
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.13 — Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family Family familya.4.13.2 — Sigma4 domain
Domain ID domain_idd1iw7f3
Class classa — All alpha proteins
Fold Fold folda.177 — Sigma2 domain of RNA polymerase sigma factors
Superfamily Superfamily superfamilya.177.1 — Sigma2 domain of RNA polymerase sigma factors
Family Family familya.177.1.1 — Sigma2 domain of RNA polymerase sigma factors
Domain ID domain_idd1iw7k1
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_idd1iw7k2
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_idd1iw7l1
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_idd1iw7l2
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_idd1iw7m_
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_idd1iw7n_
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_idd1iw7o_
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
Domain ID domain_idd1iw7p1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.13 — Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family Family familya.4.13.1 — Sigma3 domain
Domain ID domain_idd1iw7p2
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.13 — Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family Family familya.4.13.2 — Sigma4 domain
Domain ID domain_idd1iw7p3
Class classa — All alpha proteins
Fold Fold folda.177 — Sigma2 domain of RNA polymerase sigma factors
Superfamily Superfamily superfamilya.177.1 — Sigma2 domain of RNA polymerase sigma factors
Family Family familya.177.1.1 — Sigma2 domain of RNA polymerase sigma factors

CATH v4.4 (41 domains)

Domain ID domain_id1iw7A01
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_id1iw7A02
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_id1iw7B01
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_id1iw7B02
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_id1iw7C01
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_id1iw7C02
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_id1iw7C03
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_id1iw7C04
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_id1iw7C05
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_id1iw7C06
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_id1iw7D03
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_id1iw7D04
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1iw7D05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology40 — Ribonucleotide Reductase Protein R1; domain 1
Homologous superfamily homologous superfamily90 —
Domain ID domain_id1iw7D06
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_id1iw7D07
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_id1iw7D09
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology105 — Molybdopterin biosynthesis moea protein, domain 2
Homologous superfamily homologous superfamily10 — Molybdopterin biosynthesis moea protein, domain 2
Domain ID domain_id1iw7D10
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_id1iw7D11
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily280 —
Domain ID domain_id1iw7D12
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1410 —
Domain ID domain_id1iw7E00
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_id1iw7F01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily1810 —
Domain ID domain_id1iw7F02
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_id1iw7F03
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_id1iw7K01
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_id1iw7K02
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_id1iw7L01
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_id1iw7L02
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_id1iw7M01
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_id1iw7M02
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_id1iw7M03
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_id1iw7M04
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_id1iw7M05
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_id1iw7M06
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_id1iw7N03
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_id1iw7N04
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1iw7N05
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_id1iw7N06
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_id1iw7O00
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_id1iw7P01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily1810 —
Domain ID domain_id1iw7P02
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_id1iw7P03
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)