Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
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Journal
IF	>30 >20 >10 >5 all

Title	Mycobacterial HelD connects RNA polymerase recycling with transcription initiation.
Journal, issue, pages	Nat Commun, Vol. 15, Issue 1, Page 8740, Year 2024
Publish date	Oct 9, 2024
Authors	Tomáš Kovaľ / Nabajyoti Borah / Petra Sudzinová / Barbora Brezovská / Hana Šanderová / Viola Vaňková Hausnerová / Alena Křenková / Martin Hubálek / Mária Trundová / Kristýna Adámková / Jarmila Dušková / Marek Schwarz / Jana Wiedermannová / Jan Dohnálek / Libor Krásný / Tomáš Kouba /
PubMed Abstract	Mycobacterial HelD is a transcription factor that recycles stalled RNAP by dissociating it from nucleic acids and, if present, from the antibiotic rifampicin. The rescued RNAP, however, must ...Mycobacterial HelD is a transcription factor that recycles stalled RNAP by dissociating it from nucleic acids and, if present, from the antibiotic rifampicin. The rescued RNAP, however, must disengage from HelD to participate in subsequent rounds of transcription. The mechanism of release is unknown. We show that HelD from Mycobacterium smegmatis forms a complex with RNAP associated with the primary sigma factor σ and transcription factor RbpA but not CarD. We solve several structures of RNAP-σ-RbpA-HelD without and with promoter DNA. These snapshots capture HelD during transcription initiation, describing mechanistic aspects of HelD release from RNAP and its protective effect against rifampicin. Biochemical evidence supports these findings, defines the role of ATP binding and hydrolysis by HelD in the process, and confirms the rifampicin-protective effect of HelD. Collectively, these results show that when HelD is present during transcription initiation, the process is protected from rifampicin until the last possible moment.
External links	Nat Commun / PubMed:39384756 / PubMed Central
Methods	EM (single particle)
Resolution	3.09 - 3.89 Å
Structure data	18128 8q3i EMDB-18128, PDB-8q3i: Mycobacterium smegmatis RNA polymerase in complex with HelD, SigA and RbpA in State I Method: EM (single particle) / Resolution: 3.11 Å 18511 8qn8 EMDB-18511, PDB-8qn8: Mycobacterium smegmatis RNA polymerase in complex with HelD, SigA and RbpA in State II Method: EM (single particle) / Resolution: 3.14 Å 18650 8qti EMDB-18650, PDB-8qti: Mycobacterium smegnatis RNAP open promoter complex with SigmaA and RbpA Method: EM (single particle) / Resolution: 3.09 Å 18656 8qu6 EMDB-18656, PDB-8qu6: Mycobacterium smegnatis RNA polymerase transcription initiation complex with SigmaA, RbpA, HelD and an upstream-fork promoter fragment Method: EM (single particle) / Resolution: 3.45 Å 18851 8r2m EMDB-18851, PDB-8r2m: Mycobacterium smegnatis RNA polymerase transcription initiation complex with SigmaA, RbpA, HelD N-terminal domain and an upstream-fork promoter fragment; State III conformation Method: EM (single particle) / Resolution: 3.44 Å 18873 8r3m EMDB-18873, PDB-8r3m: Mycobacterium smegnatis RNA polymerase transcription initiation complex with SigmaA, RbpA, HelD N-terminal, CO and PCh loop domain, and an upstream-fork promoter fragment; State III conformation Method: EM (single particle) / Resolution: 3.49 Å 18956 8r6p EMDB-18956, PDB-8r6p: Mycobacterium smegnatis RNA polymerase RP2-like transcription initiation complex with SigmaA, RbpA, HelD N-terminal domain and open promoter DNA Method: EM (single particle) / Resolution: 3.16 Å 18959 8r6r EMDB-18959, PDB-8r6r: Mycobacterium smegnatis RNA polymerase RP2-like transcription initiation complex with SigmaA, RbpA and open promoter DNA Method: EM (single particle) / Resolution: 3.89 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-MG: Unknown entry
Source	mycolicibacterium smegmatis mc2 155 (bacteria)
Keywords	TRANSCRIPTION / HelD / RNA polymerase / transcription initiation / Mycobacteria / rifampicin resistance