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- PDB-7xr2: 3.1 Angstrom cryoEM icosahedral reconstruction of mud crab reovirus -

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Basic information

Entry
Database: PDB / ID: 7xr2
Title3.1 Angstrom cryoEM icosahedral reconstruction of mud crab reovirus
Components
  • VP11
  • VP12
  • VP3
KeywordsVIRUS / Reovirus / ds-RNA virus
Function / homologyVP3 / VP11 / VP12
Function and homology information
Biological speciesScylla serrata reovirus SZ-2007
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhang, Q. / Gao, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570736 China
National Natural Science Foundation of China (NSFC)31672677 China
CitationJournal: PLoS Pathog / Year: 2023
Title: The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization.
Authors: Qinfen Zhang / Yuanzhu Gao / Matthew L Baker / Shanshan Liu / Xudong Jia / Haidong Xu / Jianguo He / Jason T Kaelber / Shaoping Weng / Wen Jiang /
Abstract: Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell ...Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell and carry out genome replication and transcription inside the virion. Several cryo-electron microscopy (cryo-EM) structures of reoviruses with 9, 10 or 11 segmented dsRNA genomes have revealed insights into genome arrangement and transcription. However, the structure and genome arrangement of 12-segmented Reovirales members remain poorly understood. Using cryo-EM, we determined the structure of mud crab reovirus (MCRV), a 12-segmented dsRNA virus that is a putative member of Reovirales in the non-turreted Sedoreoviridae family, to near-atomic resolutions with icosahedral symmetry (3.1 Å) and without imposing icosahedral symmetry (3.4 Å). These structures revealed the organization of the major capsid proteins in two layers: an outer T = 13 layer consisting of VP12 trimers and unique VP11 clamps, and an inner T = 1 layer consisting of VP3 dimers. Additionally, ten RNA dependent RNA polymerases (RdRp) were well resolved just below the VP3 layer but were offset from the 5-fold axes and arranged with D5 symmetry, which has not previously been seen in other members of Reovirales. The N-termini of VP3 were shown to adopt four unique conformations; two of which anchor the RdRps, while the other two conformations are likely involved in genome organization and capsid stability. Taken together, these structures provide a new level of understanding for capsid stabilization and genome organization of segmented dsRNA viruses.
History
DepositionMay 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP3
B: VP3
1: VP11
2: VP11
a: VP12
b: VP12
c: VP12
d: VP12
e: VP12
f: VP12
g: VP12
h: VP12
i: VP12
j: VP12
k: VP12
l: VP12
m: VP12


Theoretical massNumber of molelcules
Total (without water)628,04317
Polymers628,04317
Non-polymers00
Water00
1
A: VP3
B: VP3
1: VP11
2: VP11
a: VP12
b: VP12
c: VP12
d: VP12
e: VP12
f: VP12
g: VP12
h: VP12
i: VP12
j: VP12
k: VP12
l: VP12
m: VP12
x 60


Theoretical massNumber of molelcules
Total (without water)37,682,5611020
Polymers37,682,5611020
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP3
B: VP3
1: VP11
2: VP11
a: VP12
b: VP12
c: VP12
d: VP12
e: VP12
f: VP12
g: VP12
h: VP12
i: VP12
j: VP12
k: VP12
l: VP12
m: VP12
x 5


  • icosahedral pentamer
  • 3.14 MDa, 85 polymers
Theoretical massNumber of molelcules
Total (without water)3,140,21385
Polymers3,140,21385
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP3
B: VP3
1: VP11
2: VP11
a: VP12
b: VP12
c: VP12
d: VP12
e: VP12
f: VP12
g: VP12
h: VP12
i: VP12
j: VP12
k: VP12
l: VP12
m: VP12
x 6


  • icosahedral 23 hexamer
  • 3.77 MDa, 102 polymers
Theoretical massNumber of molelcules
Total (without water)3,768,256102
Polymers3,768,256102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein VP3


Mass: 97019.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Scylla serrata reovirus SZ-2007 / References: UniProt: E9LEU6
#2: Protein VP11


Mass: 23750.701 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Scylla serrata reovirus SZ-2007 / References: UniProt: G9BDA7
#3: Protein
VP12


Mass: 29730.963 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Scylla serrata reovirus SZ-2007 / References: UniProt: G9BDA8

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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: Scylla serrata reovirus SZ-2007 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Scylla serrata reovirus SZ-2007
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Scylla serrata
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: 75000 X / Calibrated magnification: 128440 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Calibrated defocus min: 600 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 80 K
Image recordingAverage exposure time: 1.1 sec. / Electron dose: 25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3595
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 1-16

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Processing

SoftwareName: PHENIX / Version: 1.14rc1_3161: / Classification: refinement
EM software
IDNameVersionCategory
1EMAN22.1particle selection
2SerialEM3.6image acquisition
4jspr2014CTF correction
10jspr2014initial Euler assignment
11jspr2014final Euler assignment
13jspr20143D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 58095
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58095 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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