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- PDB-7elh: In situ structure of transcriptional enzyme complex and capsid sh... -

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Basic information

Entry
Database: PDB / ID: 7elh
TitleIn situ structure of transcriptional enzyme complex and capsid shell protein of mammalian reovirus at initiation state
Components
  • (Lambda 1) x 2
  • Minor core protein mu2
  • RNA (60-MER)
  • RNA-directed RNA polymeraseRNA-dependent RNA polymerase
  • transcript RNA
KeywordsVIRAL PROTEIN/TRANSFERASE/RNA / asymmetric / mu2 / lambda3 / lambda1 / VIRUS / VIRAL PROTEIN-TRANSFERASE-RNA complex
Function / homology
Function and homology information


viral inner capsid / host cytoskeleton / 7-methylguanosine mRNA capping / viral genome replication / viral capsid / viral nucleocapsid / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / structural molecule activity / RNA binding
Similarity search - Function
Reovirus minor core protein, Mu-2 / Reovirus minor core protein Mu-2 / Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus RNA-dependent RNA polymerase lambda 3 / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / RNA-directed RNA polymerase / Lambda 1 / Minor core protein mu2
Similarity search - Component
Biological speciesMammalian orthoreovirus 3
Mammalian orthoreovirus 3 Dearing
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhou, Z.H. / Pan, M.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1S10RR23057 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1S10OD018111 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
CitationJournal: Nat Commun / Year: 2021
Title: Asymmetric reconstruction of mammalian reovirus reveals interactions among RNA, transcriptional factor µ2 and capsid proteins.
Authors: Muchen Pan / Ana L Alvarez-Cabrera / Joon S Kang / Lihua Wang / Chunhai Fan / Z Hong Zhou /
Abstract: Mammalian reovirus (MRV) is the prototypical member of genus Orthoreovirus of family Reoviridae. However, lacking high-resolution structures of its RNA polymerase cofactor μ2 and infectious ...Mammalian reovirus (MRV) is the prototypical member of genus Orthoreovirus of family Reoviridae. However, lacking high-resolution structures of its RNA polymerase cofactor μ2 and infectious particle, limits understanding of molecular interactions among proteins and RNA, and their contributions to virion assembly and RNA transcription. Here, we report the 3.3 Å-resolution asymmetric reconstruction of transcribing MRV and in situ atomic models of its capsid proteins, the asymmetrically attached RNA-dependent RNA polymerase (RdRp) λ3, and RdRp-bound nucleoside triphosphatase μ2 with a unique RNA-binding domain. We reveal molecular interactions among virion proteins and genomic and messenger RNA. Polymerase complexes in three Spinoreovirinae subfamily members are organized with different pseudo-D symmetries to engage their highly diversified genomes. The above interactions and those between symmetry-mismatched receptor-binding σ1 trimers and RNA-capping λ2 pentamers balance competing needs of capsid assembly, external protein removal, and allosteric triggering of endogenous RNA transcription, before, during and after infection, respectively.
History
DepositionApr 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
A: Minor core protein mu2
B: RNA-directed RNA polymerase
C: transcript RNA
D: Lambda 1
e: Lambda 1
E: Lambda 1
F: Lambda 1
g: Lambda 1
G: Lambda 1
H: Lambda 1
i: Lambda 1
I: Lambda 1
J: Lambda 1
k: Lambda 1
K: Lambda 1
L: Lambda 1
m: Lambda 1
M: Lambda 1
N: RNA (60-MER)
O: RNA (60-MER)
P: RNA (60-MER)
Q: RNA (60-MER)
R: RNA (60-MER)
S: RNA (60-MER)
T: RNA (60-MER)
U: RNA (60-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,703,26127
Polymers1,703,16626
Non-polymers951
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 17 molecules ABDEFGHIJKLMegikm

#1: Protein Minor core protein mu2 / Mu 2 / Mu2


Mass: 83331.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 / References: UniProt: Q6EDZ8
#2: Protein RNA-directed RNA polymerase / RNA-dependent RNA polymerase


Mass: 142449.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3
References: UniProt: A0A0B5CSU4, RNA-directed RNA polymerase
#4: Protein
Lambda 1 / / Lambda1


Mass: 122842.859 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 / References: UniProt: F1ARN3
#5: Protein
Lambda 1 / / Lambda1


Mass: 19112.762 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 / References: UniProt: F1ARN3

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RNA chain , 2 types, 9 molecules CNOPQRSTU

#3: RNA chain transcript RNA


Mass: 1263.842 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mammalian orthoreovirus 3 Dearing
#6: RNA chain
RNA (60-MER)


Mass: 19016.188 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 Dearing

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mammalian orthoreovirus 3 Dearing / Type: VIRUS / Entity ID: #1-#3, #6 / Source: NATURAL
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102966 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Details: The distance between Residue H HIS 230 and Residue H ASN 241 is 48.65 Angstrom. Authors state that the map density of this large gaps is poor. For now the large gap could not be explained. ...Details: The distance between Residue H HIS 230 and Residue H ASN 241 is 48.65 Angstrom. Authors state that the map density of this large gaps is poor. For now the large gap could not be explained. Maybe there could have been some broken points in the large gap, but no evidence has been found. However, they could make sure that the solved coordinates are correct. The cryo-EM and the X-ray (PDB-1EJ6) results could support each other.

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