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- EMDB-22166: Assembly intermediates of orthoreovirus captured in the cell -

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Basic information

Entry
Database: EMDB / ID: EMD-22166
TitleAssembly intermediates of orthoreovirus captured in the cell
Map dataDLP-pen-5 fold
Sample
  • Complex: reovirus SLP
    • Protein or peptide: Outer capsid protein mu-1
  • Protein or peptide: Outer capsid protein sigma-3
  • Protein or peptide: Inner capsid protein sigma-2
  • Protein or peptide: Inner capsid protein lambda-1
  • Protein or peptide: mRNA (guanine-N(7)-)-methyltransferase
Function / homology
Function and homology information


icosahedral viral capsid / host cell surface binding / viral inner capsid / symbiont-mediated suppression of host PKR/eIFalpha signaling / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / protein serine/threonine kinase inhibitor activity / host cell endoplasmic reticulum / 7-methylguanosine mRNA capping ...icosahedral viral capsid / host cell surface binding / viral inner capsid / symbiont-mediated suppression of host PKR/eIFalpha signaling / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / protein serine/threonine kinase inhibitor activity / host cell endoplasmic reticulum / 7-methylguanosine mRNA capping / host cell mitochondrion / viral life cycle / viral capsid / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / GTP binding / host cell plasma membrane / structural molecule activity / ATP hydrolysis activity / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Mu1 membrane penetration protein, domain I / Reovirus, outer capsid sigma 3 / Reovirus, outer capsid sigma-3 domain superfamily / Reovirus outer capsid protein, Sigma 3 / Mu1 membrane penetration protein, domain III / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Reovirus major virion structural protein Mu-1/Mu-1C (M2) ...Mu1 membrane penetration protein, domain I / Reovirus, outer capsid sigma 3 / Reovirus, outer capsid sigma-3 domain superfamily / Reovirus outer capsid protein, Sigma 3 / Mu1 membrane penetration protein, domain III / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / 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 core-spike lambda-2 / Reovirus core-spike protein lambda-2 (L2), C-terminal / Inner capsid protein lambda-1/ VP3 / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Outer capsid protein sigma-3 / Outer capsid protein mu-1 / Outer capsid protein lambda-2 / Inner capsid protein sigma-2 / mRNA (guanine-N(7)-)-methyltransferase / Inner capsid protein lambda-1
Similarity search - Component
Biological speciesMammalian orthoreovirus 3 Dearing / T1L (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 6.5 Å
AuthorsSutton G / Sun DP / Fu XF / Kotecha A / Hecksel GW / Clare DK / Zhang P / Stuart D / Boyce M
Funding support United Kingdom, United States, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)GM082251 United States
Wellcome Trust206422/Z/17/Z United Kingdom
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Assembly intermediates of orthoreovirus captured in the cell
Authors: Sutton G / Sun DP / Fu XF / Kotecha A / Hecksel GW / Clare DK / Zhang P / Stuart D / Boyce M
History
DepositionJun 15, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateSep 23, 2020-
Current statusSep 23, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.7
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 2.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xf8
  • Surface level: 2.7
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6xf8
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ztz
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22166.png

Downloads & links

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Map

FileDownload / File: emd_22166.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDLP-pen-5 fold
Voxel sizeX=Y=Z: 1.8 Å
Density
Contour LevelBy AUTHOR: 2.7 / Movie #1: 2.7
Minimum - Maximum-5.8005085 - 8.954674
Average (Standard dev.)0.054246034 (±0.43008384)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 648.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z648.000648.000648.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-5.8018.9550.054

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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: Outer capsid protein mu-1
  • Protein or peptide: Outer capsid protein sigma-3
  • Protein or peptide: Inner capsid protein sigma-2
  • Protein or peptide: Inner capsid protein lambda-1
  • Protein or peptide: mRNA (guanine-N(7)-)-methyltransferase

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Supramolecule #1: reovirus SLP

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

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Macromolecule #1: Outer capsid protein mu-1

MacromoleculeName: Outer capsid protein mu-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: T1L (virus) / Strain: Lang
Molecular weightTheoretical: 68.568648 KDa
SequenceString: PGGVPWIAIG DETSVTSPGA LRRMTSKDIP ETAIINTDNS SGAVPSESAL VPYNDEPLVV VTEHAIANFT KAEMALEFNR EFLDKLRVL SVSPKYSDLL TYVDCYVGVS ARQALNNFQK QVPVITPTRQ TMYVDSIQAA LKALEKWEID LRVAQTLLPT N VPIGEVSC ...String:
PGGVPWIAIG DETSVTSPGA LRRMTSKDIP ETAIINTDNS SGAVPSESAL VPYNDEPLVV VTEHAIANFT KAEMALEFNR EFLDKLRVL SVSPKYSDLL TYVDCYVGVS ARQALNNFQK QVPVITPTRQ TMYVDSIQAA LKALEKWEID LRVAQTLLPT N VPIGEVSC PMQSVVKLLD DQLPDDSLIR RYPKEAAVAL AKRNGGIQWM DVSEGTVMNE AVNAVAASAL APSASAPPLE EK SKLTEQA MDLVTAAEPE IIASLVPVPA PVFAIPPKPA DYNVRTLKID EATWLRMIPK TMGTLFQIQV TDNTGTNWHF NLR GGTRVV NLDQIAPMRF VLDLGGKSYK ETSWDPNGKK VGFIVFQSKI PFELWTAASQ IGQATVVNYV QLYAEDSSFT AQSI IATTS LAYNYEPEQL NKTDPEMNYY LLATFIDSAA ITPTNMTQPD VWDALLTMSP LSAGEVTVKG AVVSEVVPAE LIGSY TPES LNASLPNDAA RCMIDRASKI AEAIKIDDDA GPDEYSPNSV PIQGQLAISQ LETGYGVRIF NPKGILSKIA SRAMQA FIG DPSTIITQAA PVLSDKNNWI ALAQGVKTSL RTKSLSAGVK TAVSKLSSSE SIQNWTQGFL DKVSTHFPAP

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Macromolecule #2: Outer capsid protein sigma-3

MacromoleculeName: Outer capsid protein sigma-3 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: T1L (virus) / Strain: Lang
Molecular weightTheoretical: 41.237117 KDa
SequenceString: MEVCLPNGHQ IVDLINNAFE GRVSIYSAQE GWDKTISAQP DMMVCGGAVV CMHCLGVVGS LQRKLKHLPH HRCNQQIRHQ DYVDVQFAD RVTAHWKRGM LSFVCQMHAM MNDVSPEDLD RVRTEGGSLV ELNWLQVDPN SMFRSIHSSW TDPLQVVDDL D TKLDQYWT ...String:
MEVCLPNGHQ IVDLINNAFE GRVSIYSAQE GWDKTISAQP DMMVCGGAVV CMHCLGVVGS LQRKLKHLPH HRCNQQIRHQ DYVDVQFAD RVTAHWKRGM LSFVCQMHAM MNDVSPEDLD RVRTEGGSLV ELNWLQVDPN SMFRSIHSSW TDPLQVVDDL D TKLDQYWT ALNLMIDSSD LVPNFMMRDP SHAFNGVRLE GDARQTQFSR TFDSRSSLEW GVMVYDYSEL EHDPSKGRAY RK ELVTPAR DFGHFGLSHY SRATTPILGK MPAVFSGMLT GNCKMYPFIK GTAKLKTVRK LVDSVNHAWG VEKIRYALGP GGM TGWYNR TMQQAPIVLT PAALTMFSDT TKFGDLDYPV MIGDPMILG

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Macromolecule #3: Inner capsid protein sigma-2

MacromoleculeName: Inner capsid protein sigma-2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: T1L (virus) / Strain: Lang
Molecular weightTheoretical: 47.024016 KDa
SequenceString: ARAAFLFKTV GFGGLQNVPI NDELSSHLLR AGNSPWQLTQ FLDWISLGRG LATSALVPTA GSRYYQMSCL LSGTLQIPFR PNHRWGDIR FLRLVWSAPT LDGLVVAPPQ VLAQPALQAQ ADRVYDCDDY PFLARDPRFK HRVYQQLSAV TLLNLTGFGP I SYVRVDED ...String:
ARAAFLFKTV GFGGLQNVPI NDELSSHLLR AGNSPWQLTQ FLDWISLGRG LATSALVPTA GSRYYQMSCL LSGTLQIPFR PNHRWGDIR FLRLVWSAPT LDGLVVAPPQ VLAQPALQAQ ADRVYDCDDY PFLARDPRFK HRVYQQLSAV TLLNLTGFGP I SYVRVDED MWSGDVNQLL MNYFGHTFAE IAYTLCQASA NRPWEHDGTY ARMTQIILSL FWLSYVGVIH QQNTYRTFYF QC NRRGDAA EVWILSCSLN HSAQIRPGNR SLFVMPTSPD WNMDVNLILS STLTGCLCSG SQLPLIDNNS VPAVSRNIHG WTG RAGNQL HGFQVRRMVT EFCDRLRRDG VMTQAQQNQI EALADQTQQF KRDKLEAWAR EDDQYNQANP NSTMFRTKPF TNAQ WGRGN TGATSAAIAA LI

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Macromolecule #4: Inner capsid protein lambda-1

MacromoleculeName: Inner capsid protein lambda-1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: T1L (virus) / Strain: Lang
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

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Macromolecule #5: mRNA (guanine-N(7)-)-methyltransferase

MacromoleculeName: mRNA (guanine-N(7)-)-methyltransferase / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: mRNA (guanine-N7)-methyltransferase
Source (natural)Organism: T1L (virus) / Strain: Lang
Molecular weightTheoretical: 143.967562 KDa
SequenceString: ANVWGVRLAD SLSSPTIETR TRQYTLHDLC SDLDANPGRE PWKPLRNQRT NNIVAVQLFR PLQGLVLDTQ LYGFPGAFDD WERFMREKL RVLKYEVLRI YPISNYSNEH VNVFVANALV GAFLSNQAFY DLLPLLIIND TMIGDLLGTG ASLSQFFQSH G DVLEVAAG ...String:
ANVWGVRLAD SLSSPTIETR TRQYTLHDLC SDLDANPGRE PWKPLRNQRT NNIVAVQLFR PLQGLVLDTQ LYGFPGAFDD WERFMREKL RVLKYEVLRI YPISNYSNEH VNVFVANALV GAFLSNQAFY DLLPLLIIND TMIGDLLGTG ASLSQFFQSH G DVLEVAAG RKYLQMENYS NDDDDPPLFA KDLSDYAKAF YSDTYEVLDR FFWTHDSSAG VLVHYDKPTN GHHYLLGTLT QM VSAPPYI INATDAMLLE SCLEQFSANV RARPAQPVTR LDQCYHLRWG AQYVGEDSLT YRLGVLSLLA TNGYQLARPI PRQ LTNRWL SSFVSQIMSD GVNETPLWPQ ERYVQIAYDS PSVVDGATQY GYVRKNQLRL GMRISALQSL SDTPSPVQWL PQYT IDQAA MDEGDLMVSR LTQLPLRPDY GNIWVGDALS YYVDYNRSHR VVLSSELPQL PDTYFDGDEQ YGRSLFSLAR KIGDR SLVK DTAVLKHAYQ AIDPNTGKEY LRSRQSVAYF GASAGHSGAD QPLVIEPWIQ GKISGVPPPS SVRQFGYDVA RGAIVD LAR PFPSGDYQFV YSDVDQVVDG HDDLSISSGL VESLLSSCMH ATAPGGSFVV KINFPTRPVW HYIEQKILPN ITSYMLI KP FVTNNVELFF VAFGVHQHSS LTWTSGVYFF LVDHFYRYET LSTISRQLPS FGYVDDGSSV TGIETISIEN PGFSNMTQ A ARIGISGLCA NVGNARKSIA IYESHGARVL TITSRRSPAS ARRKSRLRYL PLIDPRSLEV QARTILPADP VLFENVSGA SPHVCLTMMY NFEVSSAVYD GDVVLDLGTG PEAKILELIP ATSPVTCVDI RPTAQPSGCW NVRTTFLELD YLSDGWITGV RGDIVTCML SLGAAAAGKS MTFDAAFQQL IKVLSKSTAN VVLVQVNCPT DVVRSIKGYL EIDSTNKRYR FPKFGRDEPY S DMDALEKI CRTAWPNCSI TWVPLSYDLR WTRLALLEST TLSSASIRIA ELMYKYMPIM RIDIHGLPME KRGNFIVGQN CS LVIPGFN AQDVFNCYFN SALAFSTEDV NAAMIPQVSA QFDATKGEWT LDMVFSDAGI YTMQALVGSN ANPVSLGSFV VDS PDVDIT DAWPAQLDFT IAGTDVDITV NPYYRLMTFV RIDGQWQIAN PDKFQFFSSA SGTLVMNVKL DIADKYLLYY IRDV QSRDV GFYIQHPLQL LNTITLPTNE DLFLSAPDMR EWAVKESGNT ICILNSQGFV LPQDWDVLTD TISWSPSIPT YIVPP GDYT LTPL

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

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Image processing

ExtractionNumber tomograms: 4 / Number images used: 625
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: emClarity / Number subtomograms used: 625

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6xf8:
DLP 5 fold

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

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