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
Author
Journal
IF	>30 >20 >10 >5 all

Title	Capsid restructuring activates semi-conservative dsRNA transcription in cystovirus ɸ6.
Journal, issue, pages	Mol Cell, Year 2026
Publish date	Jan 8, 2026
Authors	Serban L Ilca / Xiaoyu Sun / Esa-Pekka Kumpula / Katri Eskelin / David I Stuart / Minna M Poranen / Juha T Huiskonen /
PubMed Abstract	Double-stranded (ds)RNA viruses replicate and transcribe their genome within a proteinaceous viral capsid to evade host cell defenses. While Reovirales members use conservative transcription, most ...Double-stranded (ds)RNA viruses replicate and transcribe their genome within a proteinaceous viral capsid to evade host cell defenses. While Reovirales members use conservative transcription, most dsRNA viruses, including cystoviruses, utilize semi-conservative transcription, in which a newly synthesized positive strand replaces the parental positive strand, which is released as mRNA. Here, we visualize semi-conservative transcription activation in cystovirus ɸ6 double-layered particles using cryogenic electron microscopy. We observe nucleotide-triggered disassembly of the domain-swapped outer capsid layer, subsequent expansion of the inner capsid layer, and stepwise assembly of transcription complexes at the opposing poles of the spooled dsRNA genome. These complexes consist of the viral polymerases embedded into a triskelion formed by the minor protein P7, which we show as essential for continuous transcription. The packaging hexamers proximal to the transcription sites channel the viral mRNA exit. Our results define the complex molecular pathway from the quiescent state to activated semi-conservative transcription.
External links	Mol Cell / PubMed:41512857
Methods	EM (single particle)
Resolution	3.5 - 8.0 Å
Structure data	EMDB-52379: Transcribing double-layered particle of bacteriophage phi6 reconstructed with icosahedral symmetry Method: EM (single particle) / Resolution: 6.1 Å EMDB-52380: Transcribing single-layered particle of bacteriophage phi6 reconstructed with icosahedral symmetry Method: EM (single particle) / Resolution: 6.0 Å EMDB-52381: Localized reconstruction of packaging hexamer P4 from polar region of transcribing single-layered particle of bacteriophage phi6 Method: EM (single particle) / Resolution: 6.0 Å EMDB-52382: Localized reconstruction of packaging hexamer P4 from equatorial region of transcribing single-layered particle of bacteriophage phi6 Method: EM (single particle) / Resolution: 5.2 Å EMDB-52383: Localized reconstruction of packaging hexamer P4 from polar region of transcribing double-layered particle of bacteriophage phi6 Method: EM (single particle) / Resolution: 4.9 Å EMDB-52384: Localized reconstruction of packaging hexamer P4 from equatorial region of transcribing double-layered particle of bacteriophage phi6 Method: EM (single particle) / Resolution: 4.9 Å 52385 9htw EMDB-52385: Localized reconstruction consensus map of minor protein P7 from transcribing particles of bacteriophage phi6 PDB-9htw: Minor protein P7 dimer from transcribing particles of bacteriophage phi6 Method: EM (single particle) / Resolution: 4.1 Å EMDB-52386: Localized reconstruction of polymerase P2 from transcribing double-layered particle of bacteriophage phi6 in stage A1 Method: EM (single particle) / Resolution: 4.7 Å EMDB-52387: Localized reconstruction of polymerase P2 from transcribing double-layered particle of bacteriophage phi6 in stage A2 Method: EM (single particle) / Resolution: 4.7 Å EMDB-52388: Localized reconstruction of polymerase P2 from transcribing double-layered particle of bacteriophage phi6 in stage A3 Method: EM (single particle) / Resolution: 4.7 Å 52389 9i5c 9i7w EMDB-52389: Localized reconstruction of polymerase P2 from transcribing single-layered particle of bacteriophage phi6 in stage B PDB-9i5c: Inner layer protein P1 chains in transcribing particles of bacteriophage phi6 PDB-9i7w: Extended and wrapped protein P7 dimers of dimers, the P1 layer and the RNA-dependent RNA polymerase P2 in transcribing particles of bacteriophage phi6 Method: EM (single particle) / Resolution: 4.8 Å EMDB-52390: Localized reconstruction of polymerase P2 from transcribing single-layered particle of bacteriophage phi6 in stage C Method: EM (single particle) / Resolution: 4.9 Å EMDB-52391: Asymmetric reconstruction of transcribing double-layered particle of bacteriophage phi6, disassembly intermediate 1 Method: EM (single particle) / Resolution: 7.2 Å EMDB-52392: Asymmetric reconstruction of transcribing double-layered particle of bacteriophage phi6, disassembly intermediate 2 Method: EM (single particle) / Resolution: 8.0 Å EMDB-52393: Asymmetric reconstruction of transcribing double-layered particle of bacteriophage phi6, disassembly intermediate 3 Method: EM (single particle) / Resolution: 7.6 Å EMDB-52394: Asymmetric reconstruction of transcribing double-layered particle of bacteriophage phi6, disassembly intermediate 4 Method: EM (single particle) / Resolution: 6.3 Å EMDB-52395: Transcription-arrested double-layered particle of bacteriophage phi6 reconstructed with icosahedral symmetry Method: EM (single particle) / Resolution: 3.5 Å EMDB-52396: Transcription-arrested single-layered particle of bacteriophage phi6 reconstructed with icosahedral symmetry Method: EM (single particle) / Resolution: 3.5 Å EMDB-52397: Transcription-arrested double-layered particle of bacteriophage phi6 reconstructed with D3 symmetry Method: EM (single particle) / Resolution: 4.0 Å EMDB-52398: Transcription-arrested single-layered particle of bacteriophage phi6 reconstructed with D3 symmetry Method: EM (single particle) / Resolution: 4.0 Å 52399 9hu4 EMDB-52399: Localized reconstruction of asymmetric unit from transcribing double-layered particle of bacteriophage phi6 PDB-9hu4: Asymmetric unit from transcribing double-layered particle of bacteriophage phi6 Method: EM (single particle) / Resolution: 3.5 Å 52400 9hu5 EMDB-52400: Localized reconstruction of asymmetric unit from transcribing single-layered particle of bacteriophage phi6 PDB-9hu5: Asymmetric unit from transcribing single-layered particle of bacteriophage phi6 Method: EM (single particle) / Resolution: 3.7 Å 52401 9hu6 EMDB-52401: Localized reconstruction of asymmetric unit from transcribing single-layered particle of bacteriophage phi6 in an over-expanded state PDB-9hu6: Asymmetric unit from transcribing single-layered particle of bacteriophage phi6 in an over-expanded state Method: EM (single particle) / Resolution: 3.5 Å
Source	cystovirus phi6 synthetic construct (others)
Keywords	VIRUS / cystovirus / phi6 / semi-conservative transcription / cryo-EM / cryogenic electron microscopy / localized reconstruction / symmetry relaxation / dsRNA virus / bacteriophage / VIRAL PROTEIN / structural protein / inner protein layer / transcribing particle / inner protein capsid / transcribing phi6 particle