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5d4d

Crystal structure of Thermus thermophilus product complex for transcription initiation with NAD and CTP

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 Q9Z9H6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 6 DNA 2 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 （Q72L95） ;DNA (5'-D(*CP*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3') ; × 1 DNA (27-MER) × 1 MAGNESIUM ION × 5 ZINC ION × 2 CYTIDINE-5'-MONOPHOSPHATE × 1 CYTIDINE-5'-TRIPHOSPHATE × 1 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 water × 8 Consistent with all polymers
2 Protein–DNA Heteromer Protein 6 DNA 2 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 （Q72L95） ;DNA (5'-D(*CP*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3') ; × 1 DNA (27-MER) × 1 MAGNESIUM ION × 5 ZINC ION × 2 CYTIDINE-5'-TRIPHOSPHATE × 1 CYTIDINE-5'-MONOPHOSPHATE × 1 ADENOSINE MONOPHOSPHATE × 1 water × 8 Consistent with all polymers

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

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 Protein–DNA Heteromer Protein 6 DNA 2 DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） DNA-directed RNA polymerase subunit omega × 1 （Q8RQE7） RNA polymerase sigma factor SigA × 1 （Q72L95） ;DNA (5'-D(*CP*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3') ; × 1 DNA (27-MER) × 1 MAGNESIUM ION × 5 ZINC ION × 2 CYTIDINE-5'-MONOPHOSPHATE × 1 CYTIDINE-5'-TRIPHOSPHATE × 1 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 water × 8 Consistent with all polymers
2 Protein–DNA Heteromer Protein 6 DNA 2 DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） DNA-directed RNA polymerase subunit omega × 1 （Q8RQE7） RNA polymerase sigma factor SigA × 1 （Q72L95） ;DNA (5'-D(*CP*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3') ; × 1 DNA (27-MER) × 1 MAGNESIUM ION × 5 ZINC ION × 2 CYTIDINE-5'-TRIPHOSPHATE × 1 CYTIDINE-5'-MONOPHOSPHATE × 1 ADENOSINE MONOPHOSPHATE × 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 2
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 subunit beta' ;

OrganismNot specified

UniProt Q8RQE8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 6 DNA 2 DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） DNA-directed RNA polymerase subunit omega × 1 （Q8RQE7） RNA polymerase sigma factor SigA × 1 （Q72L95） ;DNA (5'-D(*CP*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3') ; × 1 DNA (27-MER) × 1 MAGNESIUM ION × 5 ZINC ION × 2 CYTIDINE-5'-MONOPHOSPHATE × 1 CYTIDINE-5'-TRIPHOSPHATE × 1 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 water × 8 Consistent with all polymers
2 Protein–DNA Heteromer Protein 6 DNA 2 DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） DNA-directed RNA polymerase subunit omega × 1 （Q8RQE7） RNA polymerase sigma factor SigA × 1 （Q72L95） ;DNA (5'-D(*CP*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3') ; × 1 DNA (27-MER) × 1 MAGNESIUM ION × 5 ZINC ION × 2 CYTIDINE-5'-TRIPHOSPHATE × 1 CYTIDINE-5'-MONOPHOSPHATE × 1 ADENOSINE MONOPHOSPHATE × 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 3
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 subunit omega

OrganismNot specified

UniProt Q8RQE7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 6 DNA 2 DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） RNA polymerase sigma factor SigA × 1 （Q72L95） ;DNA (5'-D(*CP*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3') ; × 1 DNA (27-MER) × 1 MAGNESIUM ION × 5 ZINC ION × 2 CYTIDINE-5'-MONOPHOSPHATE × 1 CYTIDINE-5'-TRIPHOSPHATE × 1 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 water × 8 Consistent with all polymers
2 Protein–DNA Heteromer Protein 6 DNA 2 DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） RNA polymerase sigma factor SigA × 1 （Q72L95） ;DNA (5'-D(*CP*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3') ; × 1 DNA (27-MER) × 1 MAGNESIUM ION × 5 ZINC ION × 2 CYTIDINE-5'-TRIPHOSPHATE × 1 CYTIDINE-5'-MONOPHOSPHATE × 1 ADENOSINE MONOPHOSPHATE × 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 4
Chains and sequence ranges Author chain E； PDBConstruct 1–99； UniProt 1–99 Author chain O； PDBConstruct 1–99； UniProt 1–99

RNA polymerase sigma factor SigA

Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)

UniProt Q72L95

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 6 DNA 2 DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） 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*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3') ; × 1 DNA (27-MER) × 1 MAGNESIUM ION × 5 ZINC ION × 2 CYTIDINE-5'-MONOPHOSPHATE × 1 CYTIDINE-5'-TRIPHOSPHATE × 1 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 water × 8 Consistent with all polymers
2 Protein–DNA Heteromer Protein 6 DNA 2 DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） 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*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3') ; × 1 DNA (27-MER) × 1 MAGNESIUM ION × 5 ZINC ION × 2 CYTIDINE-5'-TRIPHOSPHATE × 1 CYTIDINE-5'-MONOPHOSPHATE × 1 ADENOSINE MONOPHOSPHATE × 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
3eql 3eql 5d4d 5d4d 5d4e 5d4e 5tmc 5tmf 5x21 5x22 5x22 6cuu

27 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name SIGA_THET2
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F； PDBConstruct 21–443； UniProt 1–423 Author chain P； 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_id5d4d
Deposition date deposition_date2015-08-07
Structure title titleCrystal structure of Thermus thermophilus product complex for transcription initiation with NAD and CTP
Keywords keywords;RNA polymerase, transcription initiation, bacterial, NCIN, non-canonical initiating nucleotide, primer-dependent initiation, DNA, Single-Stranded, DNA-Directed RNA Polymerases, Gene Expression Regulation, Promoter Regions, Genetic, Protein Conformation, Sigma Factor, transcription-dna complex ;; transcription/dna
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.

5d4d__assembly_1__model_1

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

Download this curve (.dat)

5d4d__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.

5d4d__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）51.82 Å
Rg (electron density)52.66 Å
Total Rg52.63 Å
Atom count28432
Residues3521
Excluded volume505550 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5d4d__assembly_1__model_1 octameric （8） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5d4d__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 (15)

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6. Fold Classification (SCOP + CATH) 25 domains

CATH v4.4 (25 domains)

Domain ID domain_id5d4dA01
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_id5d4dA02
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_id5d4dB01
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_id5d4dB02
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_id5d4dC01
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_id5d4dC03
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_id5d4dC04
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_id5d4dC05
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_id5d4dC06
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_id5d4dD01
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_id5d4dD02
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_id5d4dE00
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_id5d4dF02
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_id5d4dK01
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_id5d4dK02
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_id5d4dL01
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_id5d4dL02
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_id5d4dM01
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_id5d4dM03
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_id5d4dM04
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_id5d4dM05
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_id5d4dM06
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_id5d4dN01
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_id5d4dO00
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_id5d4dP02
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)