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Structure paper

TitleConservative transcription in three steps visualized in a double-stranded RNA virus.
Journal, issue, pagesNat Struct Mol Biol, Vol. 26, Issue 11, Page 1023-1034, Year 2019
Publish dateNov 6, 2019
AuthorsYanxiang Cui / Yinong Zhang / Kang Zhou / Jingchen Sun / Z Hong Zhou /
PubMed AbstractEndogenous RNA transcription characterizes double-stranded RNA (dsRNA) viruses in the Reoviridae, a family that is exemplified by its simple, single-shelled member cytoplasmic polyhedrosis virus (CPV) ...Endogenous RNA transcription characterizes double-stranded RNA (dsRNA) viruses in the Reoviridae, a family that is exemplified by its simple, single-shelled member cytoplasmic polyhedrosis virus (CPV). Because of the lack of in situ structures of the intermediate stages of RNA-dependent RNA polymerase (RdRp) during transcription, it is poorly understood how RdRp detects environmental cues and internal transcriptional states to initiate and coordinate repeated cycles of transcript production inside the capsid. Here, we captured five high-resolution (2.8-3.5 Å) RdRp-RNA in situ structures-representing quiescent, initiation, early elongation, elongation and abortive states-under seven experimental conditions of CPV. We observed the 'Y'-form initial RNA fork in the initiation state and the complete transcription bubble in the elongation state. These structures reveal that de novo RNA transcription involves three major conformational changes during state transitions. Our results support an ouroboros model for endogenous conservative transcription in dsRNA viruses.
External linksNat Struct Mol Biol / PubMed:31695188 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 4.1 Å
Structure data

20581

6ty8

EMDB-20581, PDB-6ty8:
In situ structure of BmCPV RNA dependent RNA polymerase at quiescent state
Method: EM (single particle) / Resolution: 3.0 Å

20582

6ty9

EMDB-20582, PDB-6ty9:
In situ structure of BmCPV RNA dependent RNA polymerase at initiation state
Method: EM (single particle) / Resolution: 2.9 Å

20585

6tz0

EMDB-20585, PDB-6tz0:
In situ structure of BmCPV RNA-dependent RNA polymerase at abortive state
Method: EM (single particle) / Resolution: 2.8 Å

20586

6tz1

EMDB-20586, PDB-6tz1:
In situ structure of BmCPV RNA-dependent RNA polymerase at early-elongation state
Method: EM (single particle) / Resolution: 3.4 Å

20587

6tz2

EMDB-20587, PDB-6tz2:
In situ structure of BmCPV RNA-dependent RNA polymerase at elongation state
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-20595:
BmCPV virion
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-20596:
BmCPV virion with SAM
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-20597:
BmCPV virion with SAM and GTP
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-20598:
BmCPV virion with SAM and ATP
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-20599:
BmCPV virion with SAM, GTP, and ATP
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-20600:
BmCPV virion with SAM, GTP, ATP, and UTP
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-20601:
BmCPV virion with SAM, GTP, ATP, UTP, and CTP
Method: EM (single particle) / Resolution: 4.1 Å

Chemicals

ChemComp-GTA:
P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE

ChemComp-MG:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

ChemComp-UTP:
URIDINE 5'-TRIPHOSPHATE / UTP*YM / Uridine triphosphate

Source
  • bombyx mori cytoplasmic polyhedrosis virus
KeywordsVIRAL PROTEIN / TRANSFERASE / RdRp / TRANSFERASE/RNA / RdRp-RNA complex / Initiation / Unwinding / Cap-binding / TRANSFERASE-RNA complex / Early-elongation / Elongation / Transcription Bubble

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