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- EMDB-13149: Mammalian orthoreovirus T3SA- in complex with the neural receptor NgR1 -

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Basic information

Entry
Database: EMDB / ID: EMD-13149
TitleMammalian orthoreovirus T3SA- in complex with the neural receptor NgR1
Map datacryoEM reconstruction of T3D orthoreovirus in complex with its neural receptor NgR1
Sample
  • Complex: Mammalian orthoreovirus T3SA- in complex with the neural receptor NgR1
    • Complex: Mammalian orthoreovirus T3SA- in complex
      • Protein or peptide: T3SA- reovirus inner capsid protein lambda1
      • Protein or peptide: T3SA- reovirus inner capsid protein sigma2
      • Protein or peptide: T3SA- reovirus outer capsid protein lambda2
      • Protein or peptide: T3SA- reovirus outer capsid protein mu1
      • Protein or peptide: T3SA- reovirus outer capsid protein sigma3
    • Complex: Nogo receptor 1
      • Protein or peptide: Nogo receptor 1
KeywordsReovirus / NgR1 / complex / receptor / VIRUS
Function / homology
Function and homology information


icosahedral viral capsid / neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / negative regulation of axon regeneration / ganglioside GT1b binding / host cell surface binding / viral inner capsid / symbiont-mediated suppression of host PKR/eIFalpha signaling ...icosahedral viral capsid / neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / negative regulation of axon regeneration / ganglioside GT1b binding / host cell surface binding / viral inner capsid / symbiont-mediated suppression of host PKR/eIFalpha signaling / negative regulation of axon extension / Axonal growth inhibition (RHOA activation) / viral outer capsid / corpus callosum development / symbiont entry into host cell via permeabilization of host membrane / protein serine/threonine kinase inhibitor activity / host cell endoplasmic reticulum / positive regulation of Rho protein signal transduction / regulation of postsynapse assembly / 7-methylguanosine mRNA capping / host cell mitochondrion / axonal growth cone / viral life cycle / positive regulation of GTPase activity / axonogenesis / dendritic shaft / regulation of translation / heparin binding / mRNA guanylyltransferase activity / presynapse / signaling receptor activity / negative regulation of neuron projection development / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / perikaryon / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / cell surface receptor signaling pathway / RNA helicase activity / neuron projection / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / membrane raft / external side of plasma membrane / neuronal cell body / protein-containing complex binding / GTP binding / host cell nucleus / host cell plasma membrane / glutamatergic synapse / structural molecule activity / cell surface / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / extracellular exosome / zinc ion binding / ATP binding / membrane / plasma 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) / 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 / : / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Leucine-rich repeat / Leucine-rich repeat domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Inner capsid protein sigma-2 / Outer capsid protein sigma-3 / Outer capsid protein mu-1 / Outer capsid protein lambda-2 / Inner capsid protein lambda-1 / Reticulon-4 receptor
Similarity search - Component
Biological speciesMammalian orthoreovirus 3 Dearing / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.9 Å
AuthorsStrebl M / Sutherland DM / Yu X / Hu L / Wang Z / Prasad BVV / Stehle T / Dermody TS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI118887 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: NgR1 binding to reovirus reveals an unusual bivalent interaction and a new viral attachment protein.
Authors: Danica M Sutherland / Michael Strebl / Melanie Koehler / Olivia L Welsh / Xinzhe Yu / Liya Hu / Rita Dos Santos Natividade / Jonathan J Knowlton / Gwen M Taylor / Rodolfo A Moreno / Patrick ...Authors: Danica M Sutherland / Michael Strebl / Melanie Koehler / Olivia L Welsh / Xinzhe Yu / Liya Hu / Rita Dos Santos Natividade / Jonathan J Knowlton / Gwen M Taylor / Rodolfo A Moreno / Patrick Wörz / Zachery R Lonergan / Pavithra Aravamudhan / Camila Guzman-Cardozo / Sukhleen Kour / Udai Bhan Pandey / David Alsteens / Zhao Wang / B V Venkataram Prasad / Thilo Stehle / Terence S Dermody /
Abstract: Nogo-66 receptor 1 (NgR1) binds a variety of structurally dissimilar ligands in the adult central nervous system to inhibit axon extension. Disruption of ligand binding to NgR1 and subsequent ...Nogo-66 receptor 1 (NgR1) binds a variety of structurally dissimilar ligands in the adult central nervous system to inhibit axon extension. Disruption of ligand binding to NgR1 and subsequent signaling can improve neuron outgrowth, making NgR1 an important therapeutic target for diverse neurological conditions such as spinal crush injuries and Alzheimer's disease. Human NgR1 serves as a receptor for mammalian orthoreovirus (reovirus), but the mechanism of virus-receptor engagement is unknown. To elucidate how NgR1 mediates cell binding and entry of reovirus, we defined the affinity of interaction between virus and receptor, determined the structure of the virus-receptor complex, and identified residues in the receptor required for virus binding and infection. These studies revealed that central NgR1 surfaces form a bridge between two copies of viral capsid protein σ3, establishing that σ3 serves as a receptor ligand for reovirus. This unusual binding interface produces high-avidity interactions between virus and receptor to prime early entry steps. These studies refine models of reovirus cell-attachment and highlight the evolution of viruses to engage multiple receptors using distinct capsid components.
History
DepositionJun 30, 2021-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateSep 13, 2023-
Current statusSep 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13149.png

Downloads & links

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Map

FileDownload / File: emd_13149.map.gz / Format: CCP4 / Size: 3.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoEM reconstruction of T3D orthoreovirus in complex with its neural receptor NgR1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.74 Å/pix.
x 960 pix.
= 1670.4 Å		1.74 Å/pix.
x 960 pix.
= 1670.4 Å		1.74 Å/pix.
x 960 pix.
= 1670.4 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1
Minimum - Maximum-5.2009287 - 5.2649045
Average (Standard dev.)0.00057333807 (±0.37876755)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions960960960
Spacing960960960
CellA=B=C: 1670.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: odd half map

Fileemd_13149_half_map_1.map
Annotationodd half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: even hald map

Fileemd_13149_half_map_2.map
Annotationeven hald map
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 T3SA- in complex with the neural receptor NgR1

EntireName: Mammalian orthoreovirus T3SA- in complex with the neural receptor NgR1
Components
  • Complex: Mammalian orthoreovirus T3SA- in complex with the neural receptor NgR1
    • Complex: Mammalian orthoreovirus T3SA- in complex
      • Protein or peptide: T3SA- reovirus inner capsid protein lambda1
      • Protein or peptide: T3SA- reovirus inner capsid protein sigma2
      • Protein or peptide: T3SA- reovirus outer capsid protein lambda2
      • Protein or peptide: T3SA- reovirus outer capsid protein mu1
      • Protein or peptide: T3SA- reovirus outer capsid protein sigma3
    • Complex: Nogo receptor 1
      • Protein or peptide: Nogo receptor 1

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Supramolecule #1: Mammalian orthoreovirus T3SA- in complex with the neural receptor NgR1

SupramoleculeName: Mammalian orthoreovirus T3SA- in complex with the neural receptor NgR1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Mammalian orthoreovirus T3SA- in complex

SupramoleculeName: Mammalian orthoreovirus T3SA- in complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing

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Supramolecule #3: Nogo receptor 1

SupramoleculeName: Nogo receptor 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: T3SA- reovirus inner capsid protein lambda1

MacromoleculeName: T3SA- reovirus inner capsid protein lambda1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MKRIPRKTKG KSSGKGNDST ERADDGSSQL RDKQNNKAGP ATTEPGTSNR EQYKARPGIA SVQRATESAE MPMKNNDEGT PDKKGNTKGD LVNEHSEAKD EADEATKKQA KDTDKSKAQV TYSDTGINNA NELSRSGNVD NEGGSNQKPM STRIAEATSA IVSKHPARVG ...String:
MKRIPRKTKG KSSGKGNDST ERADDGSSQL RDKQNNKAGP ATTEPGTSNR EQYKARPGIA SVQRATESAE MPMKNNDEGT PDKKGNTKGD LVNEHSEAKD EADEATKKQA KDTDKSKAQV TYSDTGINNA NELSRSGNVD NEGGSNQKPM STRIAEATSA IVSKHPARVG LPPTASSGHG YQCHVCSAVL FSPLDLDAHV ASHGLHGNMT LTSSDIQRHI TEFISSWQNH PIVQVSADVE NKKTAQLLHA DTPRLVTWDA GLCTSFKIVP IVPAQVPQDV LAYTFFTSSY AIQSPFPEAA VSRIVVHTRW ASNVDFDRDS SVIMAPPTEN NIHLFKQLLN TETLSVRGAN PLMFRANVLH MLLEFVLDNL YLNRHTGFSQ DHTPFTEGAN LRSLPGPDAE KWYSIMYPTR MGTPNVSKIC NFVASCVRNR VGRFDRAQMM NGAMSEWVDV FETSDALTVS IRGRWMARLA RMNINPTEIE WALTECAQGY VTVTSPYAPI VNRLMPYRIS NAERQISQII RIMNIGNNAT VIQPVLQDIS VLLQRISPLQ IDPTIISNTM STVSESTTQT LSPASSILGK LRPSNSDFSS FRVALAGWLY NGVVTTVIDD SSYPKDGGSV TSLENLWDFF ILALALPLTT DPCAPVKAFM TLANMMVGFE TIPMDNQIYT QSRRASAFST PHTWPRCFMN IQLISPIDAP ILRQWAEIIH RYWPNPSQIR YGAPNVFGSA NLFTPPEVLL LPIDHQPANV TTPTLDFTNE LTNWRARVCE LMKNLVDNQR YQPGWTQSLV SSMRGTLDKL KLIKSMTPMY LQQLAPVELA VIAPMLPFPP FQVPYVRLDR DRVPTMVGVT RQSRDTITQP ALSLSTTNTT VGVPLALDAR AITVALLSGK YPPDLVTNVW YADAIYPMYA DTEVFSNLQR DMITCEAVQT LVTLVAQISE TQYPVDRYLD WIPSLRASAA TAATFAEWVN TSMKTAFDLS DMLLEPLLSG DPRMTQLAIQ YQQYNGRTFN IIPEMPGSVI ADCVQLTAEV FNHEYNLFGI ARGDIIIGRV QSTHLWSPLA PPPDLVFDRD TPGVHIFGRD CRISFGMNGA APMIRDETGL MVPFEGNWIF PLALWQMNTR YFNQQFDAWI KTGELRIRIE MGAYPYMLHY YDPRQYANAW NLTSAWLEEI TPTSIPSVPF MVPISSDHDI SSAPAVQYII STEYNDRSLF CTNSSSPQTI AGPDKHIPVE RYNILTNPDA PPTQIQLPEV VDLYNVVTRY AYETPPITAV VMGVP

UniProtKB: Inner capsid protein lambda-1

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Macromolecule #2: T3SA- reovirus inner capsid protein sigma2

MacromoleculeName: T3SA- reovirus inner capsid protein sigma2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MARAAFLFKT VGFGGLQNVP INDELSSHLL RAGNSPWQLT QFLDWISLGR GLATSALVPT AGSRYYQMSC LLSGTLQIPF RPNHRWGDIR FLRLVWSAPT LDGLVVAPPQ VLAQPALQAQ ADRVYDCDDY PFLARDPRFK HRVYQQLSAV TLLNLTGFGP ISYVRVDEDM ...String:
MARAAFLFKT VGFGGLQNVP INDELSSHLL RAGNSPWQLT QFLDWISLGR GLATSALVPT AGSRYYQMSC LLSGTLQIPF RPNHRWGDIR FLRLVWSAPT LDGLVVAPPQ VLAQPALQAQ ADRVYDCDDY PFLARDPRFK HRVYQQLSAV TLLNLTGFGP ISYVRVDEDM WSGDVNQLLM NYFGHTFAEI AYTLCQASAN RPWEYDGTYA RMTQIVLSLF WLSYVGVIHQ QNTYRTFYFQ CNRRGDAAEV WILSCSLNHS AQIRPGNRSL FVMPTSPDWN MDVNLILSST LTGCLCSGSQ LPLIDNNSVP AVSRNIHGWT GRAGNQLHGF QVRRMVTEFC DRLRRDGVMT QAQQNQVEAL ADQTQQFKRD KLETWAREDD QYNQAHPNST MFRTKPFTNA QWGRGNTGAT SAAIAALI

UniProtKB: Inner capsid protein sigma-2

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Macromolecule #3: T3SA- reovirus outer capsid protein lambda2

MacromoleculeName: T3SA- reovirus outer capsid protein lambda2 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MANVWGVRLA DSLSSPTIET RTRQYTLHDL CSDLDANPGR EPWKPLRNQR TNNIVAVQLF RPLQGLVLDT QLYGFPGAFD DWERFMREKL RVLKYEVLRI YPISNYSNEH VNVFVANALV GAFLSNQAFY DLLPLLIIND TMIGDLLGTG ASLSQFFQSH GDVLEVAAGR ...String:
MANVWGVRLA DSLSSPTIET RTRQYTLHDL CSDLDANPGR EPWKPLRNQR TNNIVAVQLF RPLQGLVLDT QLYGFPGAFD DWERFMREKL RVLKYEVLRI YPISNYSNEH VNVFVANALV GAFLSNQAFY DLLPLLIIND TMIGDLLGTG ASLSQFFQSH GDVLEVAAGR KYLQMENYSN DDDDPPLFAK DLSDYAKAFY SDTYEVLDRF FWTHDSSAGV LVHYDKPTNG HHYLLGTLTQ MVSAPPYIIN ATDAMLLESC LEQFSANVRA RPAQPVTRLD QCYHLRWGAQ YVGEDSLTYR LGVLSLLATN GYQLARPIPR QLTNRWLSSF VSQIMSDGVN ETPLWPQERY VQIAYDSPSV VDGATQYGYV RKNQLRLGMR ISALQSLSDT PSPVQWLPQY TIDQAAMDEG DLMVSRLTQL PLRPDYGNIW VGDALSYYVD YNRSHRVVLS SELPQLPDTY FDGDEQYGRS LFSLARKIGD RSLVKDTAVL KHAYQAIDPN TGKEYLRSRQ SVAYFGASAG HSGADQPLVI EPWIQGKISG VPPPSSVRQF GYDVARGAIV DLARPFPSGD YQFVYSDVDQ VVDGHDDLSI SSGLVESLLS SCMHATAPGG SFVVKINFPT RPVWHYIEQK ILPNITSYML IKPFVTNNVE LFFVAFGVHQ HSSLTWTSGV YFFLVDHFYR YETLSTISRQ LPSFGYVDDG SSVTGIETIS IENPGFSNMT QAARIGISGL CANVGNARKS IAIYESHGAR VLTITSRRSP ASARRKSRLR YLPLIDPRSL EVQARTILPA DPVLFENVSG ASPHVCLTMM YNFEVSSAVY DGDVVLDLGT GPEAKILELI PATSPVTCVD IRPTAQPSGC WNVRTTFLEL DYLSDGWITG VRGDIVTCML SLGAAAAGKS MTFDAAFQQL IKVLSKSTAN VVLVQVNCPT DVVRSIKGYL EIDSTNKRYR FPKFGRDEPY SDMDALEKIC RTAWPNCSIT WVPLSYDLRW TRLALLESTT LSSASIRIAE LMYKYMPIMR IDIHGLPMEK RGNFIVGQNC SLVIPGFNAQ DVFNCYFNSA LAFSTEDVNA AMIPQVSAQF DATKGEWTLD MVFSDAGIYT MQALVGSNAN PVSLGSFVVD SPDVDITDAW PAQLDFTIAG TDVDITVNPY YRLMTFVRID GQWQIANPDK FQFFSSASGT LVMNVKLDIA DKYLLYYIRD VQSRDVGFYI QHPLQLLNTI TLPTNEDLFL SAPDMREWAV KESGNTICIL NSQGFVLPQD WDVLTDTISW SPSIPTYIVP PGDYTLTPL

UniProtKB: Outer capsid protein lambda-2

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Macromolecule #4: T3SA- reovirus outer capsid protein mu1

MacromoleculeName: T3SA- reovirus outer capsid protein mu1 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MGNASSIVQT INVTGDGNVF KPSAETSSTA VPSLSLSPGM LNPGGVPWIA VGDETSVTSP GALRRMTSKD IPETAIINTD NSSGAVPSES ALVPYIDEPL VVVTEHAITN FTKAEMALEF NREFLDKMRV LSVSPKYSDL LTYVDCYVGV SARQALNNFQ KQVPVITPTR ...String:
MGNASSIVQT INVTGDGNVF KPSAETSSTA VPSLSLSPGM LNPGGVPWIA VGDETSVTSP GALRRMTSKD IPETAIINTD NSSGAVPSES ALVPYIDEPL VVVTEHAITN FTKAEMALEF NREFLDKMRV LSVSPKYSDL LTYVDCYVGV SARQALNNFQ KQVPVITPTR QTMYVDSIQA ALKALEKWEI DLRVAQTLLP TNVPIGEVSC PMQSVVKLLD DQLPDDSLIR RYPKEAAVAL AKRNGGIQWM DVSEGTVMNE AVNAVAASAL APSASAPPLE EKSKLTEQAM DLVTAAEPEI IASLAPVPAP VFAIPPKPAD YNVRTLRIDE ATWLRMIPKS MNTPFQIQVT DNTGTNWHLN LRGGTRVVNL DQIAPMRFVL DLGGKSYKET SWDPNGKKVG FIVFQSKIPF ELWTAASQIG QATVVNYVQL YAEDSSFTAQ SIIATTSLAY NYEPEQLNKT DPEMNYYLLA TFIDSAAITP TNMTQPDVWD ALLTMSPLSA GEVTVKGAVV SEVVPADLIG SYTPESLNAS LPNDAARCMI DRASKIAEAI KIDDDAGPDE YSPNSVPIQG QLAISQLETG YGVRIFNPKG ILSKIASRAM QAFIGDPSTI ITQAAPVLSD KNNWIALAQG VKTSLRTKSL SAGVKTAVSK LSSSESIQNW TQGFLDKVSA HFPAPKPDCP TSGDSGESSN RRVKRDSYAG VVKRGYTR

UniProtKB: Outer capsid protein mu-1

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Macromolecule #5: T3SA- reovirus outer capsid protein sigma3

MacromoleculeName: T3SA- reovirus outer capsid protein sigma3 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Mammalian orthoreovirus 3 Dearing
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MEVCLPNGHQ VVDLINNAFE GRVSIYSAQE GWDKTISAQP DMMVCGGAVV CMHCLGVVGS LQRKLKHLPH HRCNQQIRHQ DYVDVQFADR VTAHWKRGML SFVAQMHEMM NDVSPDDLDR VRTEGGSLVE LNWLQVDPNS MFRSIHSSWT DPLQVVDDLD TKLDQYWTAL ...String:
MEVCLPNGHQ VVDLINNAFE GRVSIYSAQE GWDKTISAQP DMMVCGGAVV CMHCLGVVGS LQRKLKHLPH HRCNQQIRHQ DYVDVQFADR VTAHWKRGML SFVAQMHEMM NDVSPDDLDR VRTEGGSLVE LNWLQVDPNS MFRSIHSSWT DPLQVVDDLD TKLDQYWTAL NLMIDSSDLI PNFMMRDPSH AFNGVKLGGD ARQTQFSRTF DSRSSLEWGV MVYDYSELEH DPSKGRAYRK ELVTPARDFG HFGLSHYSRA TTPILGKMPA VFSGMLTGNC KMYPFIKGTA KLKTVRKLVE AVNHAWGVEK IRYALGPGGM TGWYNRTMQQ APIVLTPAAL TMFPDTIKFG DLNYPVMIGD PMILG

UniProtKB: Outer capsid protein sigma-3

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Macromolecule #6: Nogo receptor 1

MacromoleculeName: Nogo receptor 1 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKRASAGGSR LLAWVLWLQA WQVAAPCPGA CVCYNEPKVT TSCPQQGLQA VPVGIPAASQ RIFLHGNRIS HVPAASFRAC RNLTILWLHS NVLARIDAAA FTGLALLEQL DLSDNAQLRS VDPATFHGLG RLHTLHLDRC GLQELGPGLF RGLAALQYLY LQDNALQALP ...String:
MKRASAGGSR LLAWVLWLQA WQVAAPCPGA CVCYNEPKVT TSCPQQGLQA VPVGIPAASQ RIFLHGNRIS HVPAASFRAC RNLTILWLHS NVLARIDAAA FTGLALLEQL DLSDNAQLRS VDPATFHGLG RLHTLHLDRC GLQELGPGLF RGLAALQYLY LQDNALQALP DDTFRDLGNL THLFLHGNRI SSVPERAFRG LHSLDRLLLH QNRVAHVHPH AFRDLGRLMT LYLFANNLSA LPTEALAPLR ALQYLRLNDN PWVCDCRARP LWAWLQKFRG SSSEVPCSLP QRLAGRDLKR LAANDLQGCA HHHHHHH

UniProtKB: Reticulon-4 receptor

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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 / Component - Name: PBS
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3.5 seconds before plunging.

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Electron microscopy

MicroscopeJEOL 3200FSC
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 27.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm

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Image processing

Particle selectionNumber selected: 7182
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.31) / Number images used: 1648
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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