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- PDB-8fjl: Golden Shiner Reovirus Core Tropical Vertex -

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Basic information

Entry
Database: PDB / ID: 8fjl
TitleGolden Shiner Reovirus Core Tropical Vertex
Components
  • (Major inner capsid protein ...) x 2
  • Clamp protein VP6
  • Microtubule-associated protein VP5
  • Outer capsid protein VP1
  • RNA (30-MER)
  • RNA (38-MER)
  • RNA (39-MER)
  • RNA (52-MER)
  • RNA (60-MER)
  • RNA-directed RNA polymerase VP2
KeywordsVIRUS / dsRNA / RNA-dependent / RNA-polymerase
Function / homology
Function and homology information


viral intermediate capsid / T=2 icosahedral viral capsid / viral inner capsid / host cytoskeleton / viral outer capsid / 7-methylguanosine mRNA capping / viral genome replication / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase ...viral intermediate capsid / T=2 icosahedral viral capsid / viral inner capsid / host cytoskeleton / viral outer capsid / 7-methylguanosine mRNA capping / viral genome replication / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / viral nucleocapsid / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA helicase activity / hydrolase activity / RNA helicase / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / GTP binding / structural molecule activity / ATP hydrolysis activity / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Sigma1/sigma2, reoviral / Reoviral Sigma1/Sigma2 family / : / : / : / : / : / : / : / : ...Sigma1/sigma2, reoviral / Reoviral Sigma1/Sigma2 family / : / : / : / : / : / : / : / : / Reovirus core-spike protein lambda-2 (L2), 6th domain / Reovirus core-spike protein lambda-2 (L2), 7th domain / Reovirus core-spike protein lambda-2 (L2), ferredoxin-like domain / Reovirus core-spike protein lambda-2 (L2), GTase domain / Reovirus core-spike protein lambda-2 (L2), N-terminal / Reovirus core-spike protein lambda-2 (L2), methyltransferase-1 / Reovirus core-spike protein lambda-2 (L2), methyltransferase-2 / Reovirus minor core protein, Mu-2 / Reovirus minor core protein Mu-2 / Reovirus core-spike lambda-2 / Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus core-spike protein lambda-2 (L2), C-terminal / Reovirus RNA-dependent RNA polymerase lambda 3 / Inner capsid protein lambda-1/ VP3 / C2H2-type zinc finger / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Clamp protein VP6 / Microtubule-associated protein VP5 / Major inner capsid protein VP3 / RNA-directed RNA polymerase VP2 / Outer capsid protein VP1
Similarity search - Component
Biological speciesGolden shiner reovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsStevens, A.S. / Zhou, Z.H.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI007323 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
CitationJournal: Protein Cell / Year: 2023
Title: Asymmetric reconstruction of the aquareovirus core at near-atomic resolution and mechanism of transcription initiation.
Authors: Alexander Stevens / Yanxiang Cui / Sakar Shivakoti / Z Hong Zhou /
History
DepositionDec 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase VP2
B: Microtubule-associated protein VP5
C: Major inner capsid protein VP3
D: Major inner capsid protein VP3
E: Major inner capsid protein VP3
F: Major inner capsid protein VP3
G: Major inner capsid protein VP3
H: Major inner capsid protein VP3
I: Major inner capsid protein VP3
J: Major inner capsid protein VP3
K: Major inner capsid protein VP3
L: Major inner capsid protein VP3
M: Major inner capsid protein VP3
N: Major inner capsid protein VP3
a5: RNA (38-MER)
b5: RNA (38-MER)
b6: RNA (30-MER)
a6: RNA (30-MER)
a1: RNA (52-MER)
b1: RNA (52-MER)
a3: RNA (39-MER)
V: Clamp protein VP6
W: Clamp protein VP6
X: Clamp protein VP6
Y: Outer capsid protein VP1
Z: Outer capsid protein VP1
a: Clamp protein VP6
b: Clamp protein VP6
c: Outer capsid protein VP1
d: Clamp protein VP6
e: Clamp protein VP6
f: Outer capsid protein VP1
g: Clamp protein VP6
h: Clamp protein VP6
i: Outer capsid protein VP1
b3: RNA (39-MER)
k: Major inner capsid protein VP3
l: Major inner capsid protein VP3
m: Major inner capsid protein VP3
n: Clamp protein VP6
a2: RNA (60-MER)
b2: RNA (60-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,802,40246
Polymers2,802,14042
Non-polymers2624
Water00
1


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

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Components

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Protein , 4 types, 17 molecules ABVWXabdeghnYZcfi

#1: Protein RNA-directed RNA polymerase VP2


Mass: 141605.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Golden shiner reovirus / References: UniProt: Q8JU61, RNA-directed RNA polymerase
#2: Protein Microtubule-associated protein VP5


Mass: 79347.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Golden shiner reovirus / References: UniProt: Q8JU58
#9: Protein
Clamp protein VP6


Mass: 44489.391 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Golden shiner reovirus / References: UniProt: Q8JU54
#10: Protein
Outer capsid protein VP1


Mass: 141109.750 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Golden shiner reovirus
References: UniProt: Q8JU62, mRNA guanylyltransferase, mRNA (guanine-N7)-methyltransferase

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Major inner capsid protein ... , 2 types, 15 molecules CDEFGHIJKLMNklm

#3: Protein
Major inner capsid protein VP3 / ATP-dependent DNA helicase VP3


Mass: 124694.531 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Golden shiner reovirus / References: UniProt: Q8JU60, RNA helicase
#4: Protein
Major inner capsid protein VP3 / ATP-dependent DNA helicase VP3


Mass: 9147.655 Da / Num. of mol.: 5 / Fragment: N-terminal residues 13-106 / Source method: isolated from a natural source / Source: (natural) Golden shiner reovirus / References: UniProt: Q8JU60, RNA helicase

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RNA chain , 5 types, 10 molecules a5b5b6a6a1b1a3b3a2b2

#5: RNA chain RNA (38-MER)


Mass: 8850.246 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Golden shiner reovirus
#6: RNA chain RNA (30-MER)


Mass: 12027.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Golden shiner reovirus
#7: RNA chain RNA (52-MER)


Mass: 16474.699 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Golden shiner reovirus
#8: RNA chain RNA (39-MER)


Mass: 12662.472 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Golden shiner reovirus
#11: RNA chain RNA (60-MER)


Mass: 19016.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Golden shiner reovirus

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Non-polymers , 1 types, 4 molecules

#12: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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: Golden shiner reovirus / Type: VIRUS / Details: Virus cultured in fathead minnow cells / Entity ID: #1-#11 / Source: NATURAL
Molecular weightValue: 47 MDa / Experimental value: NO
Source (natural)Organism: Golden shiner reovirus
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Notemigonus crysoleucas
Buffer solutionpH: 7.4 / Details: Phosphate buffered saline
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 FIELD / Nominal magnification: 81000 X / Calibrated magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.5/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package
EM software
IDNameCategory
2SerialEMimage acquisition
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 99323
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99323 / Symmetry type: POINT

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