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- EMDB-22165: Assembly intermediates of orthoreovirus captured in the cell -

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Basic information

Entry
Database: EMDB / ID: EMD-22165
TitleAssembly intermediates of orthoreovirus captured in the cell
Map dataSLP
Sample
  • Complex: reovirus SLP
    • Protein or peptide: Lambda 1 protein
KeywordsVIRUS LIKE PARTICLE
Function / homology
Function and homology information


viral inner capsid / 7-methylguanosine mRNA capping / RNA helicase activity / hydrolase activity / RNA helicase / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
: / Inner capsid protein lambda-1/VP3 / Inner capsid protein lambda-1/ VP3 / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Lambda-1 / Lambda 1 protein / Inner capsid protein lambda-1
Similarity search - Component
Biological speciesMammalian orthoreovirus 3 Dearing / Mammalian orthoreovirus
Methodsubtomogram averaging / cryo EM / Resolution: 6.6 Å
AuthorsSutton G / Sun DP
Funding support United Kingdom, United States, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
Wellcome Trust206422/Z/17/Z United Kingdom
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)GM082251 United States
CitationJournal: Nat Commun / Year: 2020
Title: Assembly intermediates of orthoreovirus captured in the cell.
Authors: Geoff Sutton / Dapeng Sun / Xiaofeng Fu / Abhay Kotecha / Corey W Hecksel / Daniel K Clare / Peijun Zhang / David I Stuart / Mark Boyce /
Abstract: Traditionally, molecular assembly pathways for viruses are inferred from high resolution structures of purified stable intermediates, low resolution images of cell sections and genetic approaches. ...Traditionally, molecular assembly pathways for viruses are inferred from high resolution structures of purified stable intermediates, low resolution images of cell sections and genetic approaches. Here, we directly visualise an unsuspected 'single shelled' intermediate for a mammalian orthoreovirus in cryo-preserved infected cells, by cryo-electron tomography of cellular lamellae. Particle classification and averaging yields structures to 5.6 Å resolution, sufficient to identify secondary structural elements and produce an atomic model of the intermediate, comprising 120 copies each of protein λ1 and σ2. This λ1 shell is 'collapsed' compared to the mature virions, with molecules pushed inwards at the icosahedral fivefolds by ~100 Å, reminiscent of the first assembly intermediate of certain prokaryotic dsRNA viruses. This supports the supposition that these viruses share a common ancestor, and suggests mechanisms for the assembly of viruses of the Reoviridae. Such methodology holds promise for dissecting the replication cycle of many viruses.
History
DepositionJun 15, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xf7
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zts
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6xf7
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zts
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22165.png

Downloads & links

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Map

FileDownload / File: emd_22165.map.gz / Format: CCP4 / Size: 221.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSLP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.8 Å/pix.
x 387 pix.
= 696.6 Å		1.8 Å/pix.
x 387 pix.
= 696.6 Å		1.8 Å/pix.
x 387 pix.
= 696.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-5.906315 - 10.926515999999999
Average (Standard dev.)0.05899449 (±0.49774188)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions387387387
Spacing387387387
CellA=B=C: 696.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z387387387
origin x/y/z0.0000.0000.000
length x/y/z696.600696.600696.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS387387387
D min/max/mean-5.90610.9270.059

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Supplemental data

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Sample components

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Entire : reovirus SLP

EntireName: reovirus SLP
Components
  • Complex: reovirus SLP
    • Protein or peptide: Lambda 1 protein

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Supramolecule #1: reovirus SLP

SupramoleculeName: reovirus SLP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing

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Macromolecule #1: Lambda 1 protein

MacromoleculeName: Lambda 1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mammalian orthoreovirus
Molecular weightTheoretical: 119.020562 KDa
SequenceString: QRHITEFISS WQNHPIVQVS ADVENKKTAQ LLHADTPRLV TWDAGLCTSF KIVPIVPAQV PQDVLAYTFF TSSYAIQSPF PEAAVSRIV VHTRWASNVD FDRDSSVIMA PPTENNIHLF KQLLNTETLS VRGANPLMFR ANVLHMLLEF VLDNLYLNRH T GFSQDHTP ...String:
QRHITEFISS WQNHPIVQVS ADVENKKTAQ LLHADTPRLV TWDAGLCTSF KIVPIVPAQV PQDVLAYTFF TSSYAIQSPF PEAAVSRIV VHTRWASNVD FDRDSSVIMA PPTENNIHLF KQLLNTETLS VRGANPLMFR ANVLHMLLEF VLDNLYLNRH T GFSQDHTP FTEGANLRSL PGPDAEKWYS IMYPTRMGTP NVSKICNFVA SCVRNRVGRF DRAQMMNGAM SEWVDVFETS DA LTVSIRG RWMARLARMN INPTEIEWAL TECAQGYVTV TSPYAPSVNR LMPYRISNAE RQISQIIRIM NIGNNATVIQ PVL QDISVL LQRISPLQID PTIISNTMST VSESTTQTLS PASSILGKLR PSNSDFSSFR VALAGWLYNG VVTTVIDDSS YPKD GGSVT SLENLWDFFI LALALPLTTD PCAPVKAFMT LANMMVGFET IPMDNQIYTQ SRRASAFSTP HTWPRCFMNI QLISP IDAP ILRQWAEIIH RYWPNPSQIR YGAPNVFGSA NLFTPPEVLL LPIDHQPANV TTPTLDFTNE LTNWRARVCE LMKNLV DNQ RYQPGWTQSL VSSMRGTLDK LKLIKSMTPM YLQQLAPVEL AVIAPMLPFP PFQVPYVRLD RDRVPTMVGV TRQSRDT IT QPALSLSTTN TTVGVPLALD ARAITVALLS GKYPPDLVTN VWYADAIYPM YADTEVFSNL QRDMITCEAV QTLVTLVA Q ISETQYPVDR YLDWIPSLRA SAATAATFAE WVNTSMKTAF DLSDMLLEPL LSGDPRMTQL AIQYQQYNGR TFNVIPEMP GSVIADCVQL TAEVFNHEYN LFGIARGDII IGRVQSTHLW SPLAPPPDLV FDRDTPGVHI FGRDCRISFG MNGAAPMIRD ETGMMVPFE GNWIFPLALW QMNTRYFNQQ FDAWIKTGEL RIRIEMGAYP YMLHYYDPRQ YANAWNLTSA WLEEITPTSI P SVPFMVPI SSDHDISSAP AVQYIISTEY NDRSLFCTNS SSPQTIAGPD KHIPVERYNI LTNPDAPPTQ IQLPEVVDLY NV VTRYAYE TPPITAVVMG VP

UniProtKB: Lambda 1 protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: emClarity / Number subtomograms used: 2683
ExtractionNumber tomograms: 4 / Number images used: 2683
Final angle assignmentType: OTHER

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6xf7:
SLP

PDB-6zts:
Assembly intermediates of orthoreovirus captured in the cell

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