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- EMDB-6968: Structure of RNA polymerase complex and genome within a dsRNA vir... -

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Basic information

Entry
Database: EMDB / ID: EMD-6968
TitleStructure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly
Map dataSymmetry-mismatch structure of aquareovirus
Sample
  • Virus: Grass carp reovirus
    • Protein or peptide: VP3
    • Protein or peptide: VP2
    • Protein or peptide: Putative core protein NTPase/VP5
Function / homology
Function and homology information


viral inner capsid / host cytoskeleton / 7-methylguanosine mRNA capping / viral genome replication / viral capsid / viral nucleocapsid / host cell cytoplasm / RNA helicase activity / RNA helicase / hydrolase activity ...viral inner capsid / host cytoskeleton / 7-methylguanosine mRNA capping / viral genome replication / viral capsid / viral nucleocapsid / host cell cytoplasm / RNA helicase activity / RNA helicase / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
Reovirus minor core protein, Mu-2 / Reovirus minor core protein Mu-2 / Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus RNA-dependent RNA polymerase lambda 3 / Inner capsid protein lambda-1/ VP3 / C2H2-type zinc finger / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / zinc finger / Zinc finger C2H2 type domain profile. ...Reovirus minor core protein, Mu-2 / Reovirus minor core protein Mu-2 / Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus RNA-dependent RNA polymerase lambda 3 / Inner capsid protein lambda-1/ VP3 / C2H2-type zinc finger / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Putative core protein NTPase/VP5 / RNA helicase / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesGrass carp reovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLiu H / Fang Q / Cheng L
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Structure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly.
Authors: Xurong Wang / Fuxian Zhang / Rui Su / Xiaowu Li / Wenyuan Chen / Qingxiu Chen / Tao Yang / Jiawei Wang / Hongrong Liu / Qin Fang / Lingpeng Cheng /
Abstract: Most double-stranded RNA (dsRNA) viruses transcribe RNA plus strands within a common innermost capsid shell. This process requires coordinated efforts by RNA-dependent RNA polymerase (RdRp) together ...Most double-stranded RNA (dsRNA) viruses transcribe RNA plus strands within a common innermost capsid shell. This process requires coordinated efforts by RNA-dependent RNA polymerase (RdRp) together with other capsid proteins and genomic RNA. Here we report the near-atomic resolution structure of the RdRp protein VP2 in complex with its cofactor protein VP4 and genomic RNA within an aquareovirus capsid using 200-kV cryoelectron microscopy and symmetry-mismatch reconstruction. The structure of these capsid proteins enabled us to observe the elaborate nonicosahedral structure within the double-layered icosahedral capsid. Our structure shows that the RdRp complex is anchored at the inner surface of the capsid shell and interacts with genomic dsRNA and four of the five asymmetrically arranged N termini of the capsid shell proteins under the fivefold axis, implying roles for these N termini in virus assembly. The binding site of the RNA end at VP2 is different from the RNA cap binding site identified in the crystal structure of orthoreovirus RdRp λ3, although the structures of VP2 and λ3 are almost identical. A loop, which was thought to separate the RNA template and transcript, interacts with an apical domain of the capsid shell protein, suggesting a mechanism for regulating RdRp replication and transcription. A conserved nucleoside triphosphate binding site was localized in our RdRp cofactor protein VP4 structure, and interactions between the VP4 and the genomic RNA were identified.
History
DepositionMay 12, 2018-
Header (metadata) releaseJul 4, 2018-
Map releaseJul 4, 2018-
UpdateJul 25, 2018-
Current statusJul 25, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5zvs
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5zvs
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6968.png

Downloads & links

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Map

FileDownload / File: emd_6968.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSymmetry-mismatch structure of aquareovirus
Voxel sizeX=Y=Z: 0.932 Å
Density
Contour LevelBy AUTHOR: 8. / Movie #1: 8
Minimum - Maximum-26.853725000000001 - 54.858490000000003
Average (Standard dev.)0.73939174 (±4.089046)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-450-450-450
Dimensions900900900
Spacing900900900
CellA=B=C: 838.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9320.9320.932
M x/y/z900900900
origin x/y/z0.0000.0000.000
length x/y/z838.800838.800838.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-450-450-450
NC/NR/NS900900900
D min/max/mean-26.85454.8580.739

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Supplemental data

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Sample components

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Entire : Grass carp reovirus

EntireName: Grass carp reovirus
Components
  • Virus: Grass carp reovirus
    • Protein or peptide: VP3
    • Protein or peptide: VP2
    • Protein or peptide: Putative core protein NTPase/VP5

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Supramolecule #1: Grass carp reovirus

SupramoleculeName: Grass carp reovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 128987 / Sci species name: Grass carp reovirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host systemOrganism: Ctenopharyngodon idella (grass carp)

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Macromolecule #1: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Grass carp reovirus
Molecular weightTheoretical: 132.203312 KDa
Recombinant expressionOrganism: Ctenopharyngodon idella (grass carp)
SequenceString: MPRRSARKAQ SAIASPADTN VVPAKDAPTT NSPPSTTSPN QAAADANQQQ AGIVSSQSGP NAVGDSAPSS SVNNDGDIIT RPTSDSIAA VANATKPAAV VSDPQSMKVT PIVNPSSYVC NVCNARFSTM SALSEHLRSD HRDDASTLLA TPMINNAIRS F LTAWDDIR ...String:
MPRRSARKAQ SAIASPADTN VVPAKDAPTT NSPPSTTSPN QAAADANQQQ AGIVSSQSGP NAVGDSAPSS SVNNDGDIIT RPTSDSIAA VANATKPAAV VSDPQSMKVT PIVNPSSYVC NVCNARFSTM SALSEHLRSD HRDDASTLLA TPMINNAIRS F LTAWDDIR ILSPDVSSKS LSAYLDSAVA NGPELIIEDT GLCTSFMLLD NIPSAHLTKE LIGFTWFMQM YQMTPPLPEG AV NRIVCMT NWASLGDEGR GLEVRLPPPT DSSVHAYKTV LSRGYIDNAQ FNPLALRSNV LLMLLQFTLS NLKINKSSTF TSD VTTITS GRMIRAFEGR PELLALAYPG RAVLPTQTKN AQFLSTAIAD RIGRLDRANL IGGEVSAMVE CMELCDALTL HIRE TYIML LRSMHQDPTQ IVQIVNECAN NLLNSTIPIS LRPTILCPWF ASSEDLRLQQ VMHLVNISSN TAAALPLVEA LSTLL RSVT PLVLDPTVLT NAITTISEST TQTISPISEI LRLLQPMGND YAAFWKCIAS WAYNGLVTTV LSEDAFPDSS QSITHL PSM WKCLFLTLAG PMTSDPHSPV KVFMALANLL AQPEPIAIGV PGMHQTTPAS QFSHPGVWPP GFLNPQLINP QQAPLLR AF AEHIRANWPQ PSEFGYGSTL QGSANLFIPS NRMVYPWPNQ PLPRLTVAPT YDSAMSNWIS TTIAFFIRVV NSVNMTAT V NDLTRRTMTG VMTAMRQVKT MTPFYIQHMC PTELSVLASV TVTPPFQVPF TRLVQNDVIT NVLVARVDPA QRGDAAVDI RATHATFAAA LPVDPAAIVV AMLCGQTETN LIPSHHYGKA FAPLFASNAM FTRNQRAVIT REAFVCARSA VAQCQDAGFL VPRPLDALR QFDVTSAAAA EIMHAVNDAF KTAFDLDGAL LDGLALYGDP RIADLSAAYL QYGGNVVREH VPPGPSHIHR A LQQVESTF MAEMNLFNVA RGNLYLVQTA TNGNWSPMAP VAAPPFVRGG PNVRVVGRFG TIVPRPNGLE PQLIDDGNVP RD IAGDWVY PSDVLQVSVA VFRDYVWPMV KAGRTRVLVE LGHYVYTLHY YDPQISLDEA PILEEWLSKI NPAGIPPVPF CIP IPQVYP CITARRVHYA FTSENNNDSL FSTNAASIDT AFGENAAVSP LRWPGLVDPN YRVGTNDLPN RITLYNSLYR YNFT YPTLD GIMYVRSAT

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Grass carp reovirus
Molecular weightTheoretical: 141.685438 KDa
Recombinant expressionOrganism: Ctenopharyngodon idella (grass carp)
SequenceString: MEELFNALPQ PLQQLSLALA GEIPLTDHIF EQAASTWHVQ PRSLTYKLLD HIPFATPVVV PPSIYHSLDW SKCFAVNQDR VERIPTIDN PDDVYVPNSD IGPLLTSLHT IPDYGFLHPT IENDATTLRA ERARCASTFY KIASSQARQV KLDPIRMLGF L LLVQARPR ...String:
MEELFNALPQ PLQQLSLALA GEIPLTDHIF EQAASTWHVQ PRSLTYKLLD HIPFATPVVV PPSIYHSLDW SKCFAVNQDR VERIPTIDN PDDVYVPNSD IGPLLTSLHT IPDYGFLHPT IENDATTLRA ERARCASTFY KIASSQARQV KLDPIRMLGF L LLVQARPR VPSGLVTDQP TRRDPTLSPA LHAIWQVMQY YKVAGVYYAP ALVVPSGAIW WIPPPGKRNV VSVQYLLTDL IS LAILAHM TDMSPTLELT GVLMYLRAAS SHSYAYTLLQ MKSVFPALSL RSMYRNKGFG GKAPAIEWTE PRSKYKFRWT GVT QLHDGL RPRSPSMDVP TLETLAKYEL VDIGHTIIRE RNAHPQHNHD SVRFVRDVMA LTSGMYLVRQ PTMSVLREYS QVPD IKDPI PPSAWTGPIG NVRYLLPSVQ GPARHLYDTW RAAARQIAQD PQWHDPLNQA IMRAQYVTAR GGSSASLKFA LKVTG IVLP EYDDSKVKKS SKIYQAAQIA RIAFMLLIAA IHAEVTMGIR NQVQRRARSI MPLNVIQQAI SAPHTLVANY INKHMN LST TSGSVVTDKV IPLILYASTP PNTVVNVDIK ACDASITYNY FLSVICGAMH EGFEVGNADA AFMGVPSTIV SDRRSPV AP YSRPISGLQT MVQHLADLYA AGFRYSVSDA FSSGNKFSFP TSTFPSGSTA TSTEHTANNS TMMEYFLNVH APSHVKSA S LKRILTDMTI QRNYVCQGDD GILLLPHEAA SKISADDMNE LLTCLRDYGQ LFGWNYDIDW SDTAEYLKLY ALMGCRIPN TSRHPPVGKE YAAPQTDEIW PSLIDIVIGH HLNGVTDVLN WREWLRFSWA FACYSSRGGY TNPRGQSFSA QYPWWTFVYL GIPPILLPG QTPFIHSCYM PPGDQGMFSI LNGWRDWLIS HASTTLPPLR HNHPVWGLSD VPSLLSQFGV YAGYHAAQHY R RPKPAPET ASSDSINQIT SDLTEYLFYD SALKARVMKG RYNWERLSSS LSLNVGSRVP SLFDVPGKWV AAGRDAEKPP PS SVEDMFT SLNRCIRRPT HSFSRLLELY LRVHVALGES IPLAIDPDVP QVAGADPAND DHWFKYTCLG DIPSATRNYF GES LFVGRV VSGLDVEAVD ATLLRLKILG APPEAFIAVL NGIGMSDSEA HQIAGRISLA NAQLVQIARV VHLSIPSSWM TLNT GPYIH HHAYDFKPGI TQPSAKSRDK SIWMSPILKL LCTSYAMTVA GPVRTSIVTE IDGSAAALSG NLRVWMRDV

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Macromolecule #3: Putative core protein NTPase/VP5

MacromoleculeName: Putative core protein NTPase/VP5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Grass carp reovirus
Molecular weightTheoretical: 80.381516 KDa
Recombinant expressionOrganism: Ctenopharyngodon idella (grass carp)
SequenceString: MITIVVIPTA HFSWTDTNFL NSVDYRLTSQ PKIRDRFAVY APGWLRRQLD EFSASLTASE LLQALQTIPI PVKARCLLLP KPKRFAQWL LDVPSANIWH IPVTTLRATV ASKHPSSDVY NYIPDHVPPN AEFDTVTRRV AAGRDIYVRS TKVIGAPLCL A APAKYYAG ...String:
MITIVVIPTA HFSWTDTNFL NSVDYRLTSQ PKIRDRFAVY APGWLRRQLD EFSASLTASE LLQALQTIPI PVKARCLLLP KPKRFAQWL LDVPSANIWH IPVTTLRATV ASKHPSSDVY NYIPDHVPPN AEFDTVTRRV AAGRDIYVRS TKVIGAPLCL A APAKYYAG YLSTHQLDGI YPENWAPDNF HKREFCLTIL PSLLGPRTFL LDVDADRDAS YPLSVLWPQL RALALKSRLL LP PVALLRR VVDPGLKPTW SADSDAAFRA LRLSRPSSAS KPVGFDFSAL PVVDIICLLE SEPDDHGRIA PGTRLTIHSV PTD LLTSLS IQEGVRYPLR QESGMFVHWV LLALLMSDDV TISGTRRSVK LETAHASARP FVHITVERCA SARIIDVRGS PAMY ANAVC LTLPKGSYKS TIIDTLPAMF SDLPILEQAA VIDSDALGDS LRPSFETQFL ERLENLDPNL LDRAVASILS PTSDT SDDA VTTVLDAFNA LYREIMTPAQ RARLPLLTQQ GRVLAFAHSD YELLSANIPI QVVRGSIPID HVVNLLARRN RVGGTA LQV LLDYCYRTQA SPLAPTPAGR LYKQLFGPWL MVPRLSEPLI KLRLVASAPA KVLRAAGWTI DGDPPLEVSC LCAYVTD RA AATALIERRL DSRALVTVGG DQLMFVEYAP PLPLVSIPRT FLLPVTYVVH WVPPQRVLLN GGNVSFTSGL EWTFDDDP Q VVTSTGV

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41000

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