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2o5j

Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the NTP substrate analog

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 Q5SHR6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 5 DNA 2 RNA 1 5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3' × 1 5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3' × 1 5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3' × 1 DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） DNA-directed RNA polymerase omega chain × 1 （Q8RQE7） ZINC ION × 2 MAGNESIUM ION × 2 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 water × 8 Consistent with all polymers
2 Other combination Heteromer Protein 5 DNA 2 RNA 1 5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3' × 1 5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3' × 1 5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3' × 1 DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） DNA-directed RNA polymerase omega chain × 1 （Q8RQE7） ZINC ION × 2 MAGNESIUM ION × 2 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 water × 8 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 4
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

DNA-directed RNA polymerase beta chain

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 5 DNA 2 RNA 1 5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3' × 1 5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3' × 1 5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3' × 1 DNA-directed RNA polymerase alpha chain × 2 （Q5SHR6） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） DNA-directed RNA polymerase omega chain × 1 （Q8RQE7） ZINC ION × 2 MAGNESIUM ION × 2 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 water × 8 Consistent with all polymers
2 Other combination Heteromer Protein 5 DNA 2 RNA 1 5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3' × 1 5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3' × 1 5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3' × 1 DNA-directed RNA polymerase alpha chain × 2 （Q5SHR6） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） DNA-directed RNA polymerase omega chain × 1 （Q8RQE7） ZINC ION × 2 MAGNESIUM ION × 2 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 water × 8 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 5
Chains and sequence ranges Author chain C； PDBConstruct 1–1119； UniProt 1–1119 Author chain M； PDBConstruct 1–1119； UniProt 1–1119

;DNA-directed RNA polymerase beta' chain ;

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 5 DNA 2 RNA 1 5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3' × 1 5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3' × 1 5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3' × 1 DNA-directed RNA polymerase alpha chain × 2 （Q5SHR6） DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） DNA-directed RNA polymerase omega chain × 1 （Q8RQE7） ZINC ION × 2 MAGNESIUM ION × 2 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 water × 8 Consistent with all polymers
2 Other combination Heteromer Protein 5 DNA 2 RNA 1 5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3' × 1 5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3' × 1 5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3' × 1 DNA-directed RNA polymerase alpha chain × 2 （Q5SHR6） DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） DNA-directed RNA polymerase omega chain × 1 （Q8RQE7） ZINC ION × 2 MAGNESIUM ION × 2 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 water × 8 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 6
Chains and sequence ranges Author chain D； PDBConstruct 1–1524； UniProt 1–1524 Author chain N； PDBConstruct 1–1524； UniProt 1–1524

DNA-directed RNA polymerase omega chain

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 5 DNA 2 RNA 1 5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3' × 1 5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3' × 1 5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3' × 1 DNA-directed RNA polymerase alpha chain × 2 （Q5SHR6） DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） ZINC ION × 2 MAGNESIUM ION × 2 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 water × 8 Consistent with all polymers
2 Other combination Heteromer Protein 5 DNA 2 RNA 1 5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3' × 1 5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3' × 1 5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3' × 1 DNA-directed RNA polymerase alpha chain × 2 （Q5SHR6） DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） ZINC ION × 2 MAGNESIUM ION × 2 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 water × 8 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 7
Chains and sequence ranges Author chain E； PDBConstruct 1–99； UniProt 1–99 Author chain O； PDBConstruct 1–99； UniProt 1–99

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_id2o5j
Deposition date deposition_date2006-12-06
Structure title titleCrystal structure of the T. thermophilus RNAP polymerase elongation complex with the NTP substrate analog
Keywords keywords;RNA polymerase, elongation complex, template DNA, non-template DNA, RNA transcript, NTP substrate, TRANSFERASE-DNA-RNA HYBRID COMPLEX ;; TRANSFERASE/DNA-RNA HYBRID
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.

2o5j__assembly_1__model_1

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

Download this curve (.dat)

2o5j__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.

2o5j__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）46.30 Å
Rg (electron density)46.49 Å
Total Rg46.69 Å
Atom count24290
Residues2988
Excluded volume430360 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2o5j__assembly_1__model_1 octameric （8） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2o5j__assembly_2__model_1 octameric （8） 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) 38 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd2o5jc_
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_idd2o5jd_
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_idd2o5je_
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_idd2o5jm_
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_idd2o5jn_
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_idd2o5jo_
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 (32 domains)

Domain ID domain_id2o5jA01
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_id2o5jA02
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_id2o5jB01
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_id2o5jB02
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_id2o5jC01
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_id2o5jC02
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_id2o5jC03
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_id2o5jC04
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_id2o5jC05
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_id2o5jC06
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_id2o5jD03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily20 —
Domain ID domain_id2o5jD04
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_id2o5jD05
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_id2o5jD07
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_id2o5jE00
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_id2o5jK01
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_id2o5jK02
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_id2o5jL01
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_id2o5jL02
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_id2o5jM01
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_id2o5jM02
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_id2o5jM03
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_id2o5jM04
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_id2o5jM05
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_id2o5jM06
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_id2o5jN03
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_id2o5jN04
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily20 —
Domain ID domain_id2o5jN05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology40 — Ribonucleotide Reductase Protein R1; domain 1
Homologous superfamily homologous superfamily90 —
Domain ID domain_id2o5jN07
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_id2o5jN09
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_id2o5jN10
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_id2o5jO00
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)