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- EMDB-46049: Cryo-EM structure of MRV outer shell -

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Basic information

Entry
Database: EMDB / ID: EMD-46049
TitleCryo-EM structure of MRV outer shell
Map dataMRV outer shell
Samplemammalian reovirus != Mammalian orthoreovirus 3 Dearing

mammalian reovirus

  • Virus: Mammalian orthoreovirus 3 Dearing
    • Protein or peptide: Outer capsid protein lambda-2
    • Protein or peptide: Outer capsid protein mu-1N
    • Protein or peptide: Outer capsid protein sigma-3
KeywordsMammalian reovirus / outer shell / VIRAL PROTEIN
Function / homology
Function and homology information


icosahedral viral capsid / host cell surface binding / symbiont-mediated suppression of host PKR/eIFalpha signaling / viral outer capsid / symbiont entry into host cell via permeabilization of host membrane / protein serine/threonine kinase inhibitor activity / host cell endoplasmic reticulum / host cell mitochondrion / viral life cycle / regulation of translation ...icosahedral viral capsid / host cell surface binding / symbiont-mediated suppression of host PKR/eIFalpha signaling / viral outer capsid / symbiont entry into host cell via permeabilization of host membrane / protein serine/threonine kinase inhibitor activity / host cell endoplasmic reticulum / host cell mitochondrion / viral life cycle / regulation of translation / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / GTP binding / host cell nucleus / host cell plasma membrane / structural molecule activity / RNA binding / zinc ion binding / ATP binding / membrane
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 / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Mu1 membrane penetration protein, domain III / 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 / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Mu1 membrane penetration protein, domain III / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / : / : / : / : / : / : / : / : / 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 / 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
Similarity search - Component
Biological speciesMammalian orthoreovirus 3 Dearing
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46049.png

Downloads & links

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Map

FileDownload / File: emd_46049.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMRV outer shell
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: 0.035
Minimum - Maximum-0.06119222 - 0.123710796
Average (Standard dev.)0.00500299 (±0.011228763)
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: half1

Fileemd_46049_half_map_1.map
Annotationhalf1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2

Fileemd_46049_half_map_2.map
Annotationhalf2
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 reovirus

EntireName: mammalian reovirus
Components
  • Virus: Mammalian orthoreovirus 3 Dearing
    • Protein or peptide: Outer capsid protein lambda-2
    • Protein or peptide: Outer capsid protein mu-1N
    • Protein or peptide: Outer capsid protein sigma-3

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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: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: LLC-MK2

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Macromolecule #1: Outer capsid protein lambda-2

MacromoleculeName: Outer capsid protein lambda-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: mRNA guanylyltransferase
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing
Molecular weightTheoretical: 144.098766 KDa
SequenceString: MANVWGVRLA DSLSSPTIET RTRQYTLHDL CSDLDANPGR EPWKPLRNQR TNNIVAVQLF RPLQGLVLDT QLYGFPGAFD DWERFMREK LRVLKYEVLR IYPISNYSNE HVNVFVANAL VGAFLSNQAF YDLLPLLIIN DTMIGDLLGT GASLSQFFQS H GDVLEVAA ...String:
MANVWGVRLA DSLSSPTIET RTRQYTLHDL CSDLDANPGR EPWKPLRNQR TNNIVAVQLF RPLQGLVLDT QLYGFPGAFD DWERFMREK LRVLKYEVLR IYPISNYSNE HVNVFVANAL VGAFLSNQAF YDLLPLLIIN DTMIGDLLGT GASLSQFFQS H GDVLEVAA GRKYLQMENY SNDDDDPPLF AKDLSDYAKA FYSDTYEVLD RFFWTHDSSA GVLVHYDKPT NGHHYLLGTL TQ MVSAPPY IINATDAMLL ESCLEQFSAN VRARPAQPVT RLDQCYHLRW GAQYVGEDSL TYRLGVLSLL ATNGYQLARP IPR QLTNRW LSSFVSQIMS DGVNETPLWP QERYVQIAYD SPSVVDGATQ YGYVRKNQLR LGMRISALQS LSDTPSPVQW LPQY TIDQA AMDEGDLMVS RLTQLPLRPD YGNIWVGDAL SYYVDYNRSH RVVLSSELPQ LPDTYFDGDE QYGRSLFSLA RKIGD RSLV KDTAVLKHAY QAIDPNTGKE YLRSRQSVAY FGASAGHSGA DQPLVIEPWI QGKISGVPPP SSVRQFGYDV ARGAIV DLA RPFPSGDYQF VYSDVDQVVD GHDDLSISSG LVESLLSSCM HATAPGGSFV VKINFPTRPV WHYIEQKILP NITSYML IK PFVTNNVELF FVAFGVHQHS SLTWTSGVYF FLVDHFYRYE TLSTISRQLP SFGYVDDGSS VTGIETISIE NPGFSNMT Q AARIGISGLC ANVGNARKSI AIYESHGARV LTITSRRSPA SARRKSRLRY LPLIDPRSLE VQARTILPAD PVLFENVSG ASPHVCLTMM YNFEVSSAVY DGDVVLDLGT GPEAKILELI PATSPVTCVD IRPTAQPSGC WNVRTTFLEL DYLSDGWITG VRGDIVTCM LSLGAAAAGK SMTFDAAFQQ LIKVLSKSTA NVVLVQVNCP TDVVRSIKGY LEIDSTNKRY RFPKFGRDEP Y SDMDALEK ICRTAWPNCS ITWVPLSYDL RWTRLALLES TTLSSASIRI AELMYKYMPI MRIDIHGLPM EKRGNFIVGQ NC SLVIPGF NAQDVFNCYF NSALAFSTED VNAAMIPQVS AQFDATKGEW TLDMVFSDAG IYTMQALVGS NANPVSLGSF VVD SPDVDI TDAWPAQLDF TIAGTDVDIT VNPYYRLMTF VRIDGQWQIA NPDKFQFFSS ASGTLVMNVK LDIADKYLLY YIRD VQSRD VGFYIQHPLQ LLNTITLPTN EDLFLSAPDM REWAVKESGN TICILNSQGF VLPQDWDVLT DTISWSPSIP TYIVP PGDY TLTPL

UniProtKB: Outer capsid protein lambda-2

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Macromolecule #2: Outer capsid protein mu-1N

MacromoleculeName: Outer capsid protein mu-1N / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing
Molecular weightTheoretical: 76.334273 KDa
SequenceString: MGNASSIVQT INVTGDGNVF KPSAETSSTA VPSLSLSPGM LNPGGVPWIA VGDETSVTSP GALRRMTSKD IPETAIINTD NSSGAVPSE SALVPYIDEP LVVVTEHAIT NFTKAEMALE FNREFLDKMR VLSVSPKYSD LLTYVDCYVG VSARQALNNF Q KQVPVITP ...String:
MGNASSIVQT INVTGDGNVF KPSAETSSTA VPSLSLSPGM LNPGGVPWIA VGDETSVTSP GALRRMTSKD IPETAIINTD NSSGAVPSE SALVPYIDEP LVVVTEHAIT NFTKAEMALE FNREFLDKMR VLSVSPKYSD LLTYVDCYVG VSARQALNNF Q KQVPVITP TRQTMYVDSI QAALKALEKW EIDLRVAQTL LPTNVPIGEV SCPMQSVVKL LDDQLPDDSL IRRYPKEAAV AL AKRNGGI QWMDVSEGTV MNEAVNAVAA SALAPSASAP PLEEKSKLTE QAMDLVTAAE PEIIASLAPV PAPVFAIPPK PAD YNVRTL RIDEATWLRM IPKSMNTPFQ IQVTDNTGTN WHLNLRGGTR VVNLDQIAPM RFVLDLGGKS YKETSWDPNG KKVG FIVFQ SKIPFELWTA ASQIGQATVV NYVQLYAEDS SFTAQSIIAT TSLAYNYEPE QLNKTDPEMN YYLLATFIDS AAITP TNMT QPDVWDALLT MSPLSAGEVT VKGAVVSEVV PADLIGSYTP ESLNASLPND AARCMIDRAS KIAEAIKIDD DAGPDE YSP NSVPIQGQLA ISQLETGYGV RIFNPKGILS KIASRAMQAF IGDPSTIITQ AAPVLSDKNN WIALAQGVKT SLRTKSL SA GVKTAVSKLS SSESIQNWTQ GFLDKVSAHF PAPKPDCPTS GDSGESSNRR VKRDSYAGVV KRGYTR

UniProtKB: Outer capsid protein mu-1

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Macromolecule #3: Outer capsid protein sigma-3

MacromoleculeName: Outer capsid protein sigma-3 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing
Molecular weightTheoretical: 41.168121 KDa
SequenceString: MEVCLPNGHQ VVDLINNAFE GRVSIYSAQE GWDKTISAQP DMMVCGGAVV CMHCLGVVGS LQRKLKHLPH HRCNQQIRHQ DYVDVQFAD RVTAHWKRGM LSFVAQMHEM MNDVSPDDLD RVRTEGGSLV ELNWLQVDPN SMFRSIHSSW TDPLQVVDDL D TKLDQYWT ...String:
MEVCLPNGHQ VVDLINNAFE GRVSIYSAQE GWDKTISAQP DMMVCGGAVV CMHCLGVVGS LQRKLKHLPH HRCNQQIRHQ DYVDVQFAD RVTAHWKRGM LSFVAQMHEM MNDVSPDDLD RVRTEGGSLV ELNWLQVDPN SMFRSIHSSW TDPLQVVDDL D TKLDQYWT ALNLMIDSSD LIPNFMMRDP SHAFNGVKLG GDARQTQFSR TFDSRSSLEW GVMVYDYSEL EHDPSKGRAY RK ELVTPAR DFGHFGLSHY SRATTPILGK MPAVFSGMLT GNCKMYPFIK GTAKLKTVRK LVEAVNHAWG VEKIRYALGP GGM TGWYNR TMQQAPIVLT PAALTMFPDT IKFGDLNYPV MIGDPMILG

UniProtKB: Outer capsid protein sigma-3

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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: PELCO Ultrathin Carbon with Lacey Carbon / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
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 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 12101 / 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: 39141
Startup modelType of model: EMDB MAP
EMDB ID:

31188

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 8911
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9cyt:
Cryo-EM structure of MRV outer shell

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