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- EMDB-33787: In situ structure of polymerase complex of mammalian reovirus in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-33787
TitleIn situ structure of polymerase complex of mammalian reovirus in virion
Map data
Sample
  • Complex: Mammalian orthoreovirus 3
    • Complex: RNA
      • RNA: RNA (5'-R(P*AP*CP*GP*AP*UP*UP*AP*GP*C)-3')
      • RNA: RNA (5'-R(P*GP*CP*U)-3')
      • RNA: RNA (5'-R(P*AP*UP*CP*GP*U)-3')
    • Virus: Mammalian orthoreovirus 3
      • Protein or peptide: RNA-directed RNA polymerase
      • Protein or peptide: Mu-2 protein
      • Protein or peptide: RNA helicase
      • Protein or peptide: Lambda-2 protein
  • Ligand: ZINC ION
Keywordsmammalian reovirus / cryo-em / RNA dependent RNA polymerase / transcription / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


T=2 icosahedral viral capsid / viral inner capsid / host cytoskeleton / viral outer capsid / 7-methylguanosine mRNA capping / viral genome replication / viral capsid / mRNA guanylyltransferase activity / viral nucleocapsid / host cell cytoplasm ...T=2 icosahedral viral capsid / viral inner capsid / host cytoskeleton / viral outer capsid / 7-methylguanosine mRNA capping / viral genome replication / viral capsid / mRNA guanylyltransferase activity / viral nucleocapsid / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / hydrolase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTP binding / structural molecule activity / RNA binding / ATP binding
Similarity search - Function
Reovirus minor core protein, Mu-2 / Reovirus minor core protein Mu-2 / : / : / : / : / : / : / : / : ...Reovirus minor core protein, Mu-2 / Reovirus minor core protein Mu-2 / : / : / : / : / : / : / : / : / 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 RNA-dependent RNA polymerase lambda 3 / Reovirus RNA-dependent RNA polymerase lambda 3 / : / 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 / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
RNA-directed RNA polymerase / Lambda-2 protein / Mu-2 protein / Lambda-1 protein
Similarity search - Component
Biological speciesMammalian orthoreovirus 3
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBao KY / Zhang XL / Li DY / Zhu P
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730023 China
National Natural Science Foundation of China (NSFC)31521002 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: In situ structures of polymerase complex of mammalian reovirus illuminate RdRp activation and transcription regulation.
Authors: Keyan Bao / Xueli Zhang / Dongyu Li / Wei Sun / Zhenzhao Sun / Jingfei Wang / Ping Zhu /
Abstract: Mammalian reovirus (reovirus) is a multilayered, turreted member of characterized by transcription of dsRNA genome within the innermost capsid shell. Here, we present high-resolution in situ ...Mammalian reovirus (reovirus) is a multilayered, turreted member of characterized by transcription of dsRNA genome within the innermost capsid shell. Here, we present high-resolution in situ structures of reovirus transcriptase complex in an intact double-layered virion, and in the uncoated single-layered core particles in the unloaded, reloaded, pre-elongation, and elongation states, respectively, obtained by cryo-electron microscopy and sub-particle reconstructions. At the template entry of RNA-dependent RNA polymerase (RdRp), the RNA-loading region gets flexible after uncoating resulting in the unloading of terminal genomic RNA and inactivity of transcription. However, upon adding transcriptional substrates, the RNA-loading region is recovered leading the RNAs loaded again. The priming loop in RdRp was found to play a critical role in regulating transcription, which hinders the elongation of transcript in virion and triggers the rearrangement of RdRp C-terminal domain (CTD) during elongation, resulting in splitting of template-transcript hybrid and opening of transcript exit. With the integration of these structures, a transcriptional model of reovirus with five states is proposed. Our structures illuminate the RdRp activation and regulation of the multilayered turreted reovirus.
History
DepositionJul 8, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33787.png

Downloads & links

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Map

FileDownload / File: emd_33787.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.2559276 - 2.5222487
Average (Standard dev.)0.039277155 (±0.18886527)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33787_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33787_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Mammalian orthoreovirus 3

EntireName: Mammalian orthoreovirus 3
Components
  • Complex: Mammalian orthoreovirus 3
    • Complex: RNA
      • RNA: RNA (5'-R(P*AP*CP*GP*AP*UP*UP*AP*GP*C)-3')
      • RNA: RNA (5'-R(P*GP*CP*U)-3')
      • RNA: RNA (5'-R(P*AP*UP*CP*GP*U)-3')
    • Virus: Mammalian orthoreovirus 3
      • Protein or peptide: RNA-directed RNA polymerase
      • Protein or peptide: Mu-2 protein
      • Protein or peptide: RNA helicase
      • Protein or peptide: Lambda-2 protein
  • Ligand: ZINC ION

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Supramolecule #1: Mammalian orthoreovirus 3

SupramoleculeName: Mammalian orthoreovirus 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #5-#6, #3-#4, #7, #1-#2
Source (natural)Organism: Mammalian orthoreovirus 3

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Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6, #3-#4

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Supramolecule #2: Mammalian orthoreovirus 3

SupramoleculeName: Mammalian orthoreovirus 3 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #5, #7, #1-#2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: RNA helicase

MacromoleculeName: RNA helicase / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Mammalian orthoreovirus 3
Molecular weightTheoretical: 141.801297 KDa
SequenceString: MKRIPRKTKG KSSGKGNDST SRSDDGSSQL RDKQSNKANP ATAEPGTSNC EHYKARPGIA SVQKATESAE LPMKNNDEGT PDKRGNTKG ALVNEHVEAR DEADDATKKQ AKDTEKAKAQ VTYSDTGINN ANELSRSGNV DNEGGSNQKP MSTRIAEATS A IVSKHPAR ...String:
MKRIPRKTKG KSSGKGNDST SRSDDGSSQL RDKQSNKANP ATAEPGTSNC EHYKARPGIA SVQKATESAE LPMKNNDEGT PDKRGNTKG ALVNEHVEAR DEADDATKKQ AKDTEKAKAQ VTYSDTGINN ANELSRSGNV DNEGGSNQKP MSTRIAEATS A IVSKHPAR VGLPPTASSG HGYQCHVCSA VLFSPLDLDA HVASHGLHGN MTLTSSEIQR HITEFISSWQ NHPIVQVSAD VE NRKTAQL 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 QISQIIRVMN IGNNATVIQP VLQDISVLLQ RISPLQIDPT IISNTM STV SESTTQTLSP ASSILGKLRP SNSDFSSFRV ALAGWLYNGV VTTVIDDSSY PKDGGSVTSL ENLWDFFILA LALPLTT DP CAPVKAFMTL ANMMVGFETI PMDNQIYTQS RRASAFSTPH TWPRCFMNIQ LISPIDAPIL RQWAEIIHRY WPNPSQIR Y GTPNVFGSAN LFTPPEVLLL PIDHQPANVT TPTLDFTNEL TNWRARVCEL MKNLVDNQRY QPGWTQSLVS SMRGTLGKL KLIKSMTPMY LQQLAPVELA VIAPMLPFPP FQVPYVRLDR DRVPTMVGVT RQSRDTITQP ALSLSTTNTT VGVPLALDAR AITVALLSG KYPPDLVTNV WYADAIYPMY ADTEVFSNLQ RDVITCEAVQ TLVTLVAQIS ETQYPVDRYL DWIPSLRASA A TAATFAEW VNTSMKTAFD LSDMLLEPLL SGDPRMTQLA IQYQQYNGRT FNVIPEMPGS VIADCVQLTA EVFNHEYNLF GI ARGDIII GRVQSTHLWS PLAPPPDLVF DRDTPGVHIF GRDCRISFGM NGAAPMIRDE TGMMVPFEGN WIFPLALWQM NTR YFNQQF DAWIKTGELR IRIEMGAYPY MLHYYDPRQY ANAWNLTSAW LEEITPTSIP SVPFMVPISS DHDISSAPAV QYII STEYN DRSLFCTNSS SPQTIAGPDK HIPVERYNIL TNPDAPPTQI QLPEVVDLYN VVTRYAYETP PITAVVMGVP

UniProtKB: Lambda-1 protein

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Macromolecule #2: Lambda-2 protein

MacromoleculeName: Lambda-2 protein / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Mammalian orthoreovirus 3
Molecular weightTheoretical: 143.963438 KDa
SequenceString: MANVWGVRLA DSLSSPTIET RTRHYTLHDF YSDLDASVGK EPWRPLRNQR TNEIVAVQLF RPLQGLVFDT QLYGFPGTFS QWEQFMKEK LRVLKYEVLR IYPISTYNHD RVNVFVANAL VGAFLSNQAF YDLLPLLIVN DTMISDLLGT GAALSQFFQS H GEVLEVAA ...String:
MANVWGVRLA DSLSSPTIET RTRHYTLHDF YSDLDASVGK EPWRPLRNQR TNEIVAVQLF RPLQGLVFDT QLYGFPGTFS QWEQFMKEK LRVLKYEVLR IYPISTYNHD RVNVFVANAL VGAFLSNQAF YDLLPLLIVN DTMISDLLGT GAALSQFFQS H GEVLEVAA GRKYLQMNNY SNDDDDPPLF AKDLSDYAKA FYSDTYEVLD RFFWTHDSSA GVLVHYDKPT NGNHYILGTL TQ MVSAPPH IINATDALLL ESCLEQFAAN VRARSAQPVT RLDQCYHLRW GAQYVGEDSL TYRLGVLSLL ATNGYQLARP IPK QLTNRW LSSFVSQVVS DGINETPLWP QERYVQIAYD SPSVVDGATQ YGYVRRNQLR LGMRISALQS LSDTPAPVQW LPQY TIDQV AVDEGDAMVS QLTQLPLRPD YGSIWIGEAL SYYVDYNRSH RVVLSSELPQ LPDTYFDGDE QYGRSLFSLA RKVGD RSLV KDTAVLKHAY QAIDPNTGKE YLRAGQSVAY FGASAGHSGA DQPLVIEPWM QGKISGVPPP SSVRQFGYDV AKGAIV DLA RPFPSGDYQF VYSDVDQVVD GHDDLSISSG LVESLLDSCV HATAPGGSFV MKINFPTRTV WHYIEQKILP NVTSYML IK PFVTNNVEVF FVAFGVHQQS ALTWTSGVYF FLVDHFYRYE TLSAISRQLP SFGYVDDGSS VTGIEIISIE NPGFSNMT Q AARVGISGLC ANVGNARKSI AIYESHGARV LTITSRRSPA SARRKARLRY LPLIDPRSLE VQARTILPSN PVLFDNING ASPHVCLTMM YNFEVSSAVY DGDVVLDLGT GPEAKILELI PSTSPVTCVD IRPTAQPNGC WNVRTTFLEL DYLSDGWITG VRGDIVTCM LSLGAAAAGK SMTFDAAFQQ LVRVLTRSTA NVLLIQVNCP TDVIRTIKGY LEIDQTNKRY KFPKFGRDEP Y SDMDSLER ICRAAWPNCS ITWVPLSYDL RWTKLALLES TTLSSASVRI AELMYKYMPI MRIDIHGLPM EKQGNFIVGQ NC SLVIPGF NAQDVFNCYF NSALAFSTED VNSAMIPQVT AQFDANKGEW SLDMVFSDAG IYTMQALVGS NANPVSLGSF VVD SPDVDI TDAWPAQLDF TIAGTDVDIT VNPYYRLMAF VKIDGQWQIA NPDKFQFFSS NTGTLVMNVK LDIADRYLLY YIRD VQSRD VGFYIQHPLQ LLNTITLPTN EDLFLSAPDM REWAVKESGN TICILNSPGF IPPQDWDVLT DTISWSPSLP TYVVP PGDY TLTPL

UniProtKB: Lambda-2 protein

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Macromolecule #5: RNA-directed RNA polymerase

MacromoleculeName: RNA-directed RNA polymerase / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Mammalian orthoreovirus 3
Molecular weightTheoretical: 142.472953 KDa
SequenceString: MSSMILTQFG PFIESISGIT DQSNDVFENA AKAFSMFTRS DVYKALDEIP FSEDAMLPIP PTIYTKPSHD SYYYIDALNR VRRKTYQGP DDVYVPNCSI VELLEPHETL TSYGRLSEAI ENRAKDGDSQ ARIATTYGRI AESQARQIKA PLEKFVLALL V AEAGGSLY ...String:
MSSMILTQFG PFIESISGIT DQSNDVFENA AKAFSMFTRS DVYKALDEIP FSEDAMLPIP PTIYTKPSHD SYYYIDALNR VRRKTYQGP DDVYVPNCSI VELLEPHETL TSYGRLSEAI ENRAKDGDSQ ARIATTYGRI AESQARQIKA PLEKFVLALL V AEAGGSLY DPVLQKYDEI PGLSHNCPLW CFREICRHIS GPLPDRAPYL YLSAGVFWLM SPRMTSAIPP LLSDLVNLAI LQ QTAGLDP SLVRLGVQIC LHAAASSSYA WFILKTKSIF PQNTLHSMYE SLEGGYCPNL EWLEPRSDYK FMYMGAMPLS TKY ARSAPS NDKKARELGE KYGLSSVVSE LRRRTKTYSK HDFTSVRYIR DAMACTSGIF LVRTPTETVL QEYTQSPEIK VPIP QKDWT GPIGEIRILK DTTSSIARYL YRTWYLAAAR MAAQPRTWDP LFQAIMRSQY VTARGGSGAT LRESLYAINV SLPDF KGLP VKAATKIFQA AQLANLPFSH TSVAILADTS MGLRNQVQRR PRSIMPLNVP QQQVSAPHTL TADYINYHMN LSTTSG SAV IEKVIPLGVY ASSPPNQSIN IDISACDASI TWDFFLSVIM AAIHEGVASS SIGKPFMGVP ASIVNDESVV GVRAARP IS GMQNMIQHLS KLYKRGFSYR VNDSFSPGND FTHMTTTFPS GSTATSTEHT ANNSTMMETF LTVWGPEHTD DPDVLRLM K SLTIQRNYVC QGDDGLMIID GNTAGKVNSE TIQKMLELIS KYGEEFGWKY DIAYDGTAEY LKLYFIFGCR IPNLSRHPI VGKERANSSA EEPWPAILDQ IMGIFFNGVH DGLQWQRWIR YSWALCCAFS RQRTMTGESV GYLQYPMWSF VYWGLPLVKV FGSDPWIFS WYMPTGDLGM YSWISLIRPL MTRWMVANGY VTDKCSPVFG NADYRKCFNE LKLYQGYYMA QLPRNPKKSG R AAPREVRE QFTQALSDYL MQNPELKSRV LRGRSEWEKY GAGIIHNPPS LFDVPHKWYQ GAQEAATATR EELAEMDETL MR ARKHSYS SFSKLLEAYL LVKWRMCEAR EPSVDLRLPL CAGIDPLNSD PFLKMVSVGP MLQSTRKYFA QTLFMAKTVS GLD VNAIDS ALLRLRTLGA DKKALTAQLL MVGLQESEAD ALAGKIMLQD VNTVQLARVV NLAVPDTWMS LDFDTMFKHH VKLL PKDGR HLNTDIPPRM GWLRAILRFL GAGMAMTATG VAVDIYLEDI HGGGRSLGQR FMTWMRQEGR SA

UniProtKB: RNA-directed RNA polymerase

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Macromolecule #7: Mu-2 protein

MacromoleculeName: Mu-2 protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mammalian orthoreovirus 3
Molecular weightTheoretical: 83.434266 KDa
SequenceString: MAYIAVPAVV DSRSSEAIGL LESFGVDAGS DANDVSYQDH DYVVDQLQYM LDGYEAGDVI DALVYRNWLH HSVYCLLPPK SQLLEYWKS NPSVIPDNVD RRLRKRLMLK KDLRKDDEYN QLARAFKISD VYAPLISSTT SPMTMIQNLN QGEIVYTTTD R VIGARVLL ...String:
MAYIAVPAVV DSRSSEAIGL LESFGVDAGS DANDVSYQDH DYVVDQLQYM LDGYEAGDVI DALVYRNWLH HSVYCLLPPK SQLLEYWKS NPSVIPDNVD RRLRKRLMLK KDLRKDDEYN QLARAFKISD VYAPLISSTT SPMTMIQNLN QGEIVYTTTD R VIGARVLL YAPRKYYAST LSFTMTRCVL PFGKEVSRVP HSRFNVGTFP SIATPKCSVM SGVDIESIPN EFIKLFYQRV KS IHANILN DISPQIVSDM INRKRLRVHT PSNRRAAQLM HLPYHVKRGA SHVDVYRVDV VNVLFEVVDV ADGLRSVSRK LIM HTVPVC ILELLGIEIA DYCIRQEDGM FTDWFLLLTM LSDGLTDRRT HCQYLINPSS MPPDVILNIS ITGFINRHTI DVMP DVYDF IKPIGAVLPK GSFKSTIMRV LDSISVLGVK IMPRAHVVDS DEVGEQMEPT FEHAVMEIYK GIAGVDSLDD LTKWV LNSD LVPHDDRLGQ LFQAFLPLAK DLLAPMARQF YDNSMSEGRL LTFAHADSEL LNANYFGHLL RLKIPYITEV NLMIRK NRE GGELFQLVLS YLYKMYATSA QPKWFGSLLR LLICPWLHME KLIGEADPAS TSAEIGWHVP REQLMQDGWC GCEDGFI PY VSIRAPRLVI EELMEKNWGQ YHAQVIVTDQ LVVGEPRRVS AKAVIKGNHL PVKLISRFAC FTLTSKYEMR LPCGHSTG R GAAYNARLAF RSDLA

UniProtKB: Mu-2 protein

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Macromolecule #3: RNA (5'-R(P*GP*CP*U)-3')

MacromoleculeName: RNA (5'-R(P*GP*CP*U)-3') / type: rna / ID: 3 / Details: Transcript RNA / Number of copies: 1
Source (natural)Organism: Mammalian orthoreovirus 3
Molecular weightTheoretical: 911.596 Da
SequenceString:
GCU

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Macromolecule #4: RNA (5'-R(P*AP*UP*CP*GP*U)-3')

MacromoleculeName: RNA (5'-R(P*AP*UP*CP*GP*U)-3') / type: rna / ID: 4 / Details: Encoding RNA / Number of copies: 1
Source (natural)Organism: Mammalian orthoreovirus 3
Molecular weightTheoretical: 1.546968 KDa
SequenceString:
AUCGU

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Macromolecule #6: RNA (5'-R(P*AP*CP*GP*AP*UP*UP*AP*GP*C)-3')

MacromoleculeName: RNA (5'-R(P*AP*CP*GP*AP*UP*UP*AP*GP*C)-3') / type: rna / ID: 6 / Details: Template RNA / Number of copies: 1
Source (natural)Organism: Mammalian orthoreovirus 3
Molecular weightTheoretical: 2.855767 KDa
SequenceString:
ACGAUUAGC

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50031
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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