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- EMDB-46053: Cryo-EM structure of MRV full core -

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Basic information

Entry
Database: EMDB / ID: EMD-46053
TitleCryo-EM structure of MRV full core
Map datamap of MRV core
Sample
  • Virus: Mammalian orthoreovirus 3 Dearing
    • Protein or peptide: Lambda 1
    • Protein or peptide: Outer capsid protein lambda-2
    • Protein or peptide: Inner capsid protein sigma-2
KeywordsMammalian reovirus / outer shell / VIRAL PROTEIN
Function / homology
Function and homology information


icosahedral viral capsid / viral inner capsid / viral outer capsid / 7-methylguanosine mRNA capping / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / hydrolase activity / RNA helicase activity ...icosahedral viral capsid / viral inner capsid / viral outer capsid / 7-methylguanosine mRNA capping / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / hydrolase activity / RNA helicase activity / RNA helicase / GTP binding / zinc ion binding / ATP 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 / : / Inner capsid protein lambda-1/VP3 / 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
RNA helicase / Inner capsid protein sigma-2 / Outer capsid protein lambda-2
Similarity search - Component
Biological speciesMammalian orthoreovirus 3 Dearing
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLiu XY / Xia X / Martynowycz MW / Gonen T / Zhou ZH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
CitationJournal: Nat Commun / Year: 2024
Title: Molecular sociology of virus-induced cellular condensates supporting reovirus assembly and replication.
Authors: Xiaoyu Liu / Xian Xia / Michael W Martynowycz / Tamir Gonen / Z Hong Zhou /
Abstract: Virus-induced cellular condensates, or viral factories, are poorly understood high-density phases where replication of many viruses occurs. Here, by cryogenic electron tomography (cryoET) of focused ...Virus-induced cellular condensates, or viral factories, are poorly understood high-density phases where replication of many viruses occurs. Here, by cryogenic electron tomography (cryoET) of focused ion beam (FIB) milling-produced lamellae of mammalian reovirus (MRV)-infected cells, we visualized the molecular organization and interplay (i.e., "molecular sociology") of host and virus in 3D at two time points post-infection, enabling a detailed description of these condensates and a mechanistic understanding of MRV replication within them. Expanding over time, the condensate fashions host ribosomes at its periphery, and host microtubules, lipid membranes, and viral molecules in its interior, forming a 3D architecture that supports the dynamic processes of viral genome replication and capsid assembly. A total of six MRV assembly intermediates are identified inside the condensate: star core, empty and genome-containing cores, empty and full virions, and outer shell particle. Except for star core, these intermediates are visualized at atomic resolution by cryogenic electron microscopy (cryoEM) of cellular extracts. The temporal sequence and spatial rearrangement among these viral intermediates choreograph the viral life cycle within the condensates. Together, the molecular sociology of MRV-induced cellular condensate highlights the functional advantage of transient enrichment of molecules at the right location and time for viral replication.
History
DepositionAug 2, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46053.png

Downloads & links

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Map

FileDownload / File: emd_46053.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of MRV core
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.05710162 - 0.086201645
Average (Standard dev.)0.00080410123 (±0.0064615305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half2 map of MRV core

Fileemd_46053_half_map_1.map
Annotationhalf2 map of MRV core
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1 map of MRV core

Fileemd_46053_half_map_2.map
Annotationhalf1 map of MRV core
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mammalian orthoreovirus 3 Dearing

EntireName: Mammalian orthoreovirus 3 Dearing
Components
  • Virus: Mammalian orthoreovirus 3 Dearing
    • Protein or peptide: Lambda 1
    • Protein or peptide: Outer capsid protein lambda-2
    • Protein or peptide: Inner capsid protein sigma-2

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Supramolecule #1: Mammalian orthoreovirus 3 Dearing

SupramoleculeName: Mammalian orthoreovirus 3 Dearing / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10886 / Sci species name: Mammalian orthoreovirus 3 Dearing / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: LLC-MK2

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Macromolecule #1: Lambda 1

MacromoleculeName: Lambda 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing
Molecular weightTheoretical: 141.937375 KDa
SequenceString: MKRIPRKTKG KSSGKGNDST ERADDGSSQL RDKQNNKAGP ATTEPGTSNR EQYKARPGIA SVQRATESAE MPMKNNDEGT PDKKGNTKG DLVNEHSEAK DEADEATKKQ AKDTDKSKAQ VTYSDTGINN ANELSRSGNV DNEGGSNQKP MSTRIAEATS A IVSKHPAR ...String:
MKRIPRKTKG KSSGKGNDST ERADDGSSQL RDKQNNKAGP ATTEPGTSNR EQYKARPGIA SVQRATESAE MPMKNNDEGT PDKKGNTKG DLVNEHSEAK DEADEATKKQ AKDTDKSKAQ VTYSDTGINN ANELSRSGNV DNEGGSNQKP MSTRIAEATS A IVSKHPAR VGLPPTASSG HGYQCHVCSA VLFSPLDLDA HVASHGLHGN MTLTSSDIQR HITEFISSWQ NHPIVQVSAD VE NKKTAQL LHADTPRLVT WDAGLCTSFK IVPIVPAQVP QDVLAYTFFT SSYAIQSPFP EAAVSRIVVH TRWASNVDFD RDS SVIMAP PTENNIHLFK QLLNTETLSV RGANPLMFRA NVLHMLLEFV LDNLYLNRHT GFSQDHTPFT EGANLRSLPG PDAE KWYSI MYPTRMGTPN VSKICNFVAS CVRNRVGRFD RAQMMNGAMS EWVDVFETSD ALTVSIRGRW MARLARMNIN PTEIE WALT ECAQGYVTVT SPYAPSVNRL MPYRISNAER QISQIIRIMN IGNNATVIQP VLQDISVLLQ RISPLQIDPT IISNTM STV SESTTQTLSP ASSILGKLRP SNSDFSSFRV ALAGWLYNGV VTTVIDDSSY PKDGGSVTSL ENLWDFFILA LALPLTT DP CAPVKAFMTL ANMMVGFETI PMDNQIYTQS RRASAFSTPH TWPRCFMNIQ LISPIDAPIL RQWAEIIHRY WPNPSQIR Y GAPNVFGSAN LFTPPEVLLL PIDHQPANVT TPTLDFTNEL TNWRARVCEL MKNLVDNQRY QPGWTQSLVS SMRGTLDKL KLIKSMTPMY LQQLAPVELA VIAPMLPFPP FQVPYVRLDR DRVPTMVGVT RQSRDTITQP ALSLSTTNTT VGVPLALDAR AITVALLSG KYPPDLVTNV WYADAIYPMY ADTEVFSNLQ RDMITCEAVQ TLVTLVAQIS ETQYPVDRYL DWIPSLRASA A TAATFAEW VNTSMKTAFD LSDMLLEPLL SGDPRMTQLA IQYQQYNGRT FNIIPEMPGS VIADCVQLTA EVFNHEYNLF GI ARGDIII GRVQSTHLWS PLAPPPDLVF DRDTPGVHIF GRDCRISFGM NGAAPMIRDE TGLMVPFEGN WIFPLALWQM NTR YFNQQF DAWIKTGELR IRIEMGAYPY MLHYYDPRQY ANAWNLTSAW LEEITPTSIP SVPFMVPISS DHDISSAPAV QYII STEYN DRSLFCTNSS SPQTIAGPDK HIPVERYNIL TNPDAPPTQI QLPEVVDLYN VVTRYAYETP PITAVVMGVP

UniProtKB: RNA helicase

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Macromolecule #2: Outer capsid protein lambda-2

MacromoleculeName: Outer capsid protein lambda-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: mRNA guanylyltransferase
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing
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

UniProtKB: Outer capsid protein lambda-2

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing
Molecular weightTheoretical: 47.075055 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 NRPWEYDGTY ARMTQIVLSL FWLSYVGVIH QQNTYRTFYF QC NRRGDAA EVWILSCSLN HSAQIRPGNR SLFVMPTSPD WNMDVNLILS STLTGCLCSG SQLPLIDNNS VPAVSRNIHG WTG RAGNQL HGFQVRRMVT EFCDRLRRDG VMTQAQQNQV EALADQTQQF KRDKLETWAR EDDQYNQAHP NSTMFRTKPF TNAQ WGRGN TGATSAAIAA LI

UniProtKB: Inner capsid protein sigma-2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: Phosphate-buffered saline
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 22739 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 592105
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING ONLY
Startup modelType of model: EMDB MAP
EMDB ID:

31188

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 10857
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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