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- EMDB-31184: In situ structure of capping enzyme lambda2, penetration protein ... -

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Basic information

Entry
Database: EMDB / ID: EMD-31184
TitleIn situ structure of capping enzyme lambda2, penetration protein mu1 of mammalian reovirus capsid asymmetric unit.
Map data
SampleMammalian orthoreovirus 3 Dearing:
virus / (Mu1) x 2 / mRNA (guanine-N(7)-)-methyltransferase / ligand
Function / homology
Function and homology information


mRNA guanylyltransferase activity / mRNA guanylyltransferase / host cell surface binding / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / viral entry via permeabilization of inner membrane / mRNA (guanine-N7)-methyltransferase / mRNA (guanine-N7-)-methyltransferase activity / : / GTP binding / ATP binding
Similarity search - Function
Mu1 membrane penetration protein, domain I / Reovirus core-spike lambda-2 / Reovirus core-spike protein lambda-2 (L2) / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / Mu1/VP4 superfamily / Mu1 membrane penetration protein, domain II / Immunoglobulin-like fold
Similarity search - Domain/homology
mRNA (guanine-N(7)-)-methyltransferase / Mu1
Similarity search - Component
Biological speciesMammalian orthoreovirus 3 Dearing / Mammalian orthoreovirus 3
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhou ZH / Pan M
Funding support United States, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DE025567 United States
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 12, 2021-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateOct 20, 2021-
Current statusOct 20, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ell
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ell
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_31184.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 600 pix.
= 642. Å
1.07 Å/pix.
x 600 pix.
= 642. Å
1.07 Å/pix.
x 600 pix.
= 642. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.01853774 - 0.03678633
Average (Standard dev.)0.0009727747 (±0.003815516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 642.00006 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z642.000642.000642.000
α/β/γ90.00090.00090.000
start NX/NY/NZ336210602
NX/NY/NZ227193139
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0190.0370.001

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Supplemental data

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Sample components

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Entire Mammalian orthoreovirus 3 Dearing

EntireName: Mammalian orthoreovirus 3 Dearing / Number of Components: 5

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Component #1: virus, Mammalian orthoreovirus 3 Dearing

VirusName: Mammalian orthoreovirus 3 Dearing / Class: VIRION / Empty: No / Enveloped: No / Isolate: SEROTYPE
SpeciesSpecies: Mammalian orthoreovirus 3 Dearing

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Component #2: protein, Mu1

ProteinName: Mu1 / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 4.050441 kDa
SourceSpecies: Mammalian orthoreovirus 3

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Component #3: protein, Mu1

ProteinName: Mu1 / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 72.228719 kDa
SourceSpecies: Mammalian orthoreovirus 3

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Component #4: protein, mRNA (guanine-N(7)-)-methyltransferase

ProteinName: mRNA (guanine-N(7)-)-methyltransferase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 143.998625 kDa
SourceSpecies: Mammalian orthoreovirus 3

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Component #5: ligand, MYRISTIC ACID

LigandName: MYRISTIC ACID / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 0.228371 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 56 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 61861
3D reconstructionResolution: 3.8 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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