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- EMDB-31184: In situ structure of capping enzyme lambda2, penetration protein ... -

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Basic information

Entry
Database: EMDB / ID: EMD-31184
TitleIn situ structure of capping enzyme lambda2, penetration protein mu1 of mammalian reovirus capsid asymmetric unit.
Map data
Sample
  • Virus: Mammalian orthoreovirus 3 Dearing
    • Protein or peptide: mRNA (guanine-N(7)-)-methyltransferase
  • Protein or peptide: Mu1
  • Protein or peptide: Mu1
  • Ligand: MYRISTIC ACID
Function / homology
Function and homology information


host cell surface binding / 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 / : / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / GTP binding / ATP binding
Similarity search - Function
Mu1 membrane penetration protein, domain I / 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) / Reovirus core-spike lambda-2 / Reovirus core-spike protein lambda-2 (L2), C-terminal / Immunoglobulin-like fold
Similarity search - Domain/homology
mRNA (guanine-N(7)-)-methyltransferase / Mu1
Similarity search - Component
Biological speciesMammalian orthoreovirus 3 / Mammalian orthoreovirus 3 Dearing
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhou ZH / Pan M
Funding support United States, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1S10RR23057 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1S10OD018111 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
CitationJournal: Nat Commun / Year: 2021
Title: Asymmetric reconstruction of mammalian reovirus reveals interactions among RNA, transcriptional factor µ2 and capsid proteins.
Authors: Muchen Pan / Ana L Alvarez-Cabrera / Joon S Kang / Lihua Wang / Chunhai Fan / Z Hong Zhou /
Abstract: Mammalian reovirus (MRV) is the prototypical member of genus Orthoreovirus of family Reoviridae. However, lacking high-resolution structures of its RNA polymerase cofactor μ2 and infectious ...Mammalian reovirus (MRV) is the prototypical member of genus Orthoreovirus of family Reoviridae. However, lacking high-resolution structures of its RNA polymerase cofactor μ2 and infectious particle, limits understanding of molecular interactions among proteins and RNA, and their contributions to virion assembly and RNA transcription. Here, we report the 3.3 Å-resolution asymmetric reconstruction of transcribing MRV and in situ atomic models of its capsid proteins, the asymmetrically attached RNA-dependent RNA polymerase (RdRp) λ3, and RdRp-bound nucleoside triphosphatase μ2 with a unique RNA-binding domain. We reveal molecular interactions among virion proteins and genomic and messenger RNA. Polymerase complexes in three Spinoreovirinae subfamily members are organized with different pseudo-D symmetries to engage their highly diversified genomes. The above interactions and those between symmetry-mismatched receptor-binding σ1 trimers and RNA-capping λ2 pentamers balance competing needs of capsid assembly, external protein removal, and allosteric triggering of endogenous RNA transcription, before, during and after infection, respectively.
History
DepositionApr 12, 2021-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateOct 20, 2021-
Current statusOct 20, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ell
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ell
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31184.png

Downloads & links

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Map

FileDownload / File: emd_31184.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.01853774 - 0.03678633
Average (Standard dev.)0.0009727747 (±0.003815516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 642.00006 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z642.000642.000642.000
α/β/γ90.00090.00090.000
start NX/NY/NZ336210602
NX/NY/NZ227193139
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0190.0370.001

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Supplemental data

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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: mRNA (guanine-N(7)-)-methyltransferase
  • Protein or peptide: Mu1
  • Protein or peptide: Mu1
  • Ligand: MYRISTIC ACID

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Supramolecule #1: Mammalian orthoreovirus 3 Dearing

SupramoleculeName: Mammalian orthoreovirus 3 Dearing / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #3 / NCBI-ID: 10886 / Sci species name: Mammalian orthoreovirus 3 Dearing / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Mu1

MacromoleculeName: Mu1 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Mammalian orthoreovirus 3
Molecular weightTheoretical: 4.050441 KDa
SequenceString:
GNASSIVQTI NVTGDGNVFK PSAETSSTAV PSLSLSPGML N

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Macromolecule #2: Mu1

MacromoleculeName: Mu1 / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Mammalian orthoreovirus 3
Molecular weightTheoretical: 72.228719 KDa
SequenceString: PGGVPWIAVG DETSVTSPGA LRRMTSKDIP ETAIINTDNS SGAVPSESAL VPYIDEPLVV VTEHAITNFT KAEMALEFNR EFLDKMRVL SVSPKYSDLL TYVDCYVGVS ARQALNNFQK QVPVITPTRQ TMYVDSIQAA LKALEKWEID LRVAQTLLPT N VPIGEVSC ...String:
PGGVPWIAVG DETSVTSPGA LRRMTSKDIP ETAIINTDNS SGAVPSESAL VPYIDEPLVV VTEHAITNFT KAEMALEFNR EFLDKMRVL SVSPKYSDLL TYVDCYVGVS ARQALNNFQK QVPVITPTRQ TMYVDSIQAA LKALEKWEID LRVAQTLLPT N VPIGEVSC PMQSVVKLLD DQLPDDSLIR RYPKEAAVAL AKRNGGIQWM DVSEGTVMNE AVNAVAASAL APSASAPPLE EK SKLTEQA MDLVTAAEPE IIASLVPVPA PVFAIPPKPA DYNVRTLRID EATWLRMIPK SMNTPFQIQV TDNTGTNWHL NLR GGTRVV NLDQIAPMRF VLDLGGKSYK ETSWDPNGKK VGFIVFQSKI PFELWTAASQ IGQATVVNYV QLYAEDSSFT AQSI IATTS LAYNYEPEQL NKTDPEMNYY LLATFIDSAA ITPTNMTQPD VWDALLTMSP LSAGEVTVKG AVVSEVVPAD LIGSY TPES LNTSLPNDAA RCMIDRASKI AEAIKIDDDA GPDEYSPNSV PIQGQLAISQ LETGYGVRIF NPKGILSKIA SRAMQA FIG DPSTIITQAA PVLSDKNNWI ALAQGVKTSL RTKSLSAGVK TAVSKLSSSE SIQNWTQGFL DKVSAHFPAP KPDCPTS GD SGESSNRRVK RDSYAGVVKR GYTR

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Macromolecule #3: mRNA (guanine-N(7)-)-methyltransferase

MacromoleculeName: mRNA (guanine-N(7)-)-methyltransferase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: mRNA (guanine-N7)-methyltransferase
Source (natural)Organism: Mammalian orthoreovirus 3
Molecular weightTheoretical: 143.998625 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 YLRSGQSVAY 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

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Macromolecule #4: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 4 / Number of copies: 10 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC ACID / Myristic acid

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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
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: 56.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Sphere
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61861
FSC plot (resolution estimation)

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