5uh6

Crystal structure of Mycobacterium tuberculosis transcription initiation complex containing 2ntRNA in complex with Rifampin

Method: X-RAY DIFFRACTION
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt P9WGZ1

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 (P9WGY9) ;DNA-directed RNA polymerase subunit beta' ; × 1 (P9WGY7) DNA-directed RNA polymerase subunit omega × 1 (P9WGY5) RNA polymerase sigma factor SigA × 1 (P9WGI1) ;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*G)-3') ; × 1 ;DNA (5'-D(*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*G)-3') ; × 1 ;RNA (5'-R(*GP*A)-3') ; × 1 RIFAMPICIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOA_MYCTU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–347; UniProt 1–347 Author chain B; PDBConstruct 1–347; UniProt 1–347

DNA-directed RNA polymerase subunit beta

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt P9WGY9

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 (P9WGZ1) ;DNA-directed RNA polymerase subunit beta' ; × 1 (P9WGY7) DNA-directed RNA polymerase subunit omega × 1 (P9WGY5) RNA polymerase sigma factor SigA × 1 (P9WGI1) ;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*G)-3') ; × 1 ;DNA (5'-D(*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*G)-3') ; × 1 ;RNA (5'-R(*GP*A)-3') ; × 1 RIFAMPICIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOB_MYCTU
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–1178; UniProt 1–1178

;DNA-directed RNA polymerase subunit beta' ;

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt P9WGY7

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 (P9WGZ1) DNA-directed RNA polymerase subunit beta × 1 (P9WGY9) DNA-directed RNA polymerase subunit omega × 1 (P9WGY5) RNA polymerase sigma factor SigA × 1 (P9WGI1) ;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*G)-3') ; × 1 ;DNA (5'-D(*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*G)-3') ; × 1 ;RNA (5'-R(*GP*A)-3') ; × 1 RIFAMPICIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOC_MYCTU
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–1316; UniProt 1–1316

DNA-directed RNA polymerase subunit omega

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt P9WGY5

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 (P9WGZ1) DNA-directed RNA polymerase subunit beta × 1 (P9WGY9) ;DNA-directed RNA polymerase subunit beta' ; × 1 (P9WGY7) RNA polymerase sigma factor SigA × 1 (P9WGI1) ;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*G)-3') ; × 1 ;DNA (5'-D(*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*G)-3') ; × 1 ;RNA (5'-R(*GP*A)-3') ; × 1 RIFAMPICIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPOZ_MYCTU
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E; PDBConstruct 1–110; UniProt 1–110

RNA polymerase sigma factor SigA

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt P9WGI1

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 (P9WGZ1) DNA-directed RNA polymerase subunit beta × 1 (P9WGY9) ;DNA-directed RNA polymerase subunit beta' ; × 1 (P9WGY7) DNA-directed RNA polymerase subunit omega × 1 (P9WGY5) ;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*G)-3') ; × 1 ;DNA (5'-D(*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*G)-3') ; × 1 ;RNA (5'-R(*GP*A)-3') ; × 1 RIFAMPICIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name SIGA_MYCTU
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F; PDBConstruct 1–528; UniProt 1–528

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id5uh6
Deposition date deposition_date2017-01-11
Structure title titleCrystal structure of Mycobacterium tuberculosis transcription initiation complex containing 2ntRNA in complex with Rifampin
Keywords keywordsRNA polymerase complex, transcription, DNA, RNA, TRANSCRIPTION-DNA-RNA complex, transcription-dna-rna-antibiotic complex; transcription/dna/rna/antibiotic
Experimental Method methodX-RAY DIFFRACTION
▼

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.

5uh6__assembly_1__model_1

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

Download this curve (.dat)

5uh6__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.

5uh6__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)48.11 Å
Rg (electron density)47.77 Å
Total Rg47.99 Å
Atom count26085
Residues3283
Excluded volume460680 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5uh6__assembly_1__model_1 nonameric (9) Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (11)

▼

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id5uh6A01
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_id5uh6A02
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_id5uh6B01
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_id5uh6B02
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_id5uh6D01
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_id5uh6D02
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
▶

7. Citations (1)