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Yorodumi- EMDB-6969: Structure of RNA polymerase complex and genome within a dsRNA vir... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6969 | |||||||||
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Title | Structure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly | |||||||||
Map data | Icosahedral capsid of aquareovirus | |||||||||
Sample |
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Function / homology | Function and homology information symbiont entry into host cell via permeabilization of inner membrane / viral inner capsid / host cell surface binding / permeabilization of host organelle membrane involved in viral entry into host cell / viral outer capsid / 7-methylguanosine mRNA capping / mRNA guanylyltransferase activity / viral capsid / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity ...symbiont entry into host cell via permeabilization of inner membrane / viral inner capsid / host cell surface binding / permeabilization of host organelle membrane involved in viral entry into host cell / viral outer capsid / 7-methylguanosine mRNA capping / mRNA guanylyltransferase activity / viral capsid / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / hydrolase activity / RNA helicase / GTP binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Grass carp reovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Liu H / Fang Q / Cheng L | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6969.map.gz | 2.5 GB | EMDB map data format | |
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Header (meta data) | emd-6969-v30.xml emd-6969.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
Images | emd_6969.png | 96.6 KB | ||
Masks | emd_6969_msk_1.map | 11.9 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6969 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6969 | HTTPS FTP |
-Validation report
Summary document | emd_6969_validation.pdf.gz | 639.9 KB | Display | EMDB validaton report |
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Full document | emd_6969_full_validation.pdf.gz | 639.5 KB | Display | |
Data in XML | emd_6969_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | emd_6969_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6969 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6969 | HTTPS FTP |
-Related structure data
Related structure data | 5zvtMC 6968C 5zvsC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6969.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Icosahedral capsid of aquareovirus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.932 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_6969_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Grass carp reovirus
Entire | Name: Grass carp reovirus |
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Components |
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-Supramolecule #1: Grass carp reovirus
Supramolecule | Name: Grass carp reovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 / NCBI-ID: 128987 / Sci species name: Grass carp reovirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host system | Organism: Ctenopharyngodon idella (grass carp) |
-Macromolecule #1: Outer capsid VP7
Macromolecule | Name: Outer capsid VP7 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Grass carp reovirus |
Molecular weight | Theoretical: 29.844648 KDa |
Recombinant expression | Organism: Ctenopharyngodon idella (grass carp) |
Sequence | String: MPLHMIPQVA HAMVRAAAAG RLTLYTRTRT ETTNFDHAEY VTCGRYTICA FCLTTLAPHA NVKTIQDSHA CSRQPNEAIR SLVEVSDKA QTALVGSRTV DYHELDVKAG FVAPTADETI APSKDIVELP FRTCDLDDSS ATACVRNHCQ AGHDGVIHLP I LSGDFKLP ...String: MPLHMIPQVA HAMVRAAAAG RLTLYTRTRT ETTNFDHAEY VTCGRYTICA FCLTTLAPHA NVKTIQDSHA CSRQPNEAIR SLVEVSDKA QTALVGSRTV DYHELDVKAG FVAPTADETI APSKDIVELP FRTCDLDDSS ATACVRNHCQ AGHDGVIHLP I LSGDFKLP NEHPTKPLDD THPHDKVLTR CPKTGLLLVH DTHAHATAVV ATAATRAILM HDLLTSANAD DGHQARSACY GP AFNNLTF ACHSTCASDM AHFDCGQIVG LDLHVEPSD |
-Macromolecule #2: N-terminus of outer capsid protein VP5
Macromolecule | Name: N-terminus of outer capsid protein VP5 / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Grass carp reovirus |
Molecular weight | Theoretical: 4.302686 KDa |
Recombinant expression | Organism: Ctenopharyngodon idella (grass carp) |
Sequence | String: MGNVQTSVNT YNITGDGNSF TPTSDMTSTA APAIDLKPGV LN |
-Macromolecule #3: C-terminus of outer capsid protein VP5
Macromolecule | Name: C-terminus of outer capsid protein VP5 / type: protein_or_peptide / ID: 3 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Grass carp reovirus |
Molecular weight | Theoretical: 64.362086 KDa |
Recombinant expression | Organism: Ctenopharyngodon idella (grass carp) |
Sequence | String: PTGKLWRPVG TSVATIDSLA IVSDRFGQYS FVNEGMRETF SKALFDINMW QPLFQATKTG CGPIVLSSFT TTTSGYVGAT AGDALDNPV TNGVFISTVQ IMNLQRTIAA RMRDVALWQK HLDTAMTMLT PDISAGSASC NWKSLLAFAK DILPLDNLCL T YPNEFYNV ...String: PTGKLWRPVG TSVATIDSLA IVSDRFGQYS FVNEGMRETF SKALFDINMW QPLFQATKTG CGPIVLSSFT TTTSGYVGAT AGDALDNPV TNGVFISTVQ IMNLQRTIAA RMRDVALWQK HLDTAMTMLT PDISAGSASC NWKSLLAFAK DILPLDNLCL T YPNEFYNV AIHRYPALKP GNPDTKLPDA QAHPLGEVAG AFNAATSEVG SLVGSSSTLS QAISTMAGKD LDLIEADTPL PV SVFTPSL APRSYRPAFI KPEDAKWIAE FNNSSLIRKT LTYSGATYTV QLGPGPTRVI DMNAMIDSVL TLDVSGTILP YDT NPDLST SVPAFVLIQT SVPIQQVTTA ANITAITVVS AAGASAINLA INVRGQPRFN MLHLQATFER ETITGIPYIY GLGT FLIPS PTSSSNFSNP TLMDGLLTVT PVLLRETTYK GEVVDAIVPA TVMANQTSEE VASALANDAI VLVSNHLNKL ANVVG DAIP VASRTDDSAT SAIVSRLAVQ HKLSQVGQAS PTPPDYPLLW RRAKRAASMF VSNPSLALQV GIPVLTQSGM LSALTS GVG TALRTGSLGK GVTDASEKLR ARQSLTVAKQ AFFDQIGSLW PGK |
-Macromolecule #4: Core protein VP6
Macromolecule | Name: Core protein VP6 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Grass carp reovirus |
Molecular weight | Theoretical: 44.606535 KDa |
Recombinant expression | Organism: Ctenopharyngodon idella (grass carp) |
Sequence | String: MAQRQFFGLT YNFYGQPAPL FDLNDLQELA GCYARPWTSR FSHLAISTGS LPVWSARYPS VASRNIVVNT LLGAHLNPFA GGQITSHQG ITWRDPVLSS LAPVPAIQPP PVWAVAENVL LDSNNYPTYV LNLSSMWPIN QDVHIMTMWA LSDQGPIYHL E VPVDPMPA ...String: MAQRQFFGLT YNFYGQPAPL FDLNDLQELA GCYARPWTSR FSHLAISTGS LPVWSARYPS VASRNIVVNT LLGAHLNPFA GGQITSHQG ITWRDPVLSS LAPVPAIQPP PVWAVAENVL LDSNNYPTYV LNLSSMWPIN QDVHIMTMWA LSDQGPIYHL E VPVDPMPA ATTAALMAYT GVPIAHLAQT AYRFAGQLPQ SPDSTMVSTI RWLSAIWFGS LTGRLNRSRT CNGFYFEFAK PA LNPDQAV LKWNDGARAA PPAAAQSSYI RCISPHWQHQ IVEVAGALMS QSVTAVTGLP ALIDEATLPA WSQGVANLTG NGQ GVVPCL DYNPVPMAAA RHLQWRQDGL ITAAQEAQLN NDYTAYALTI ERHLTAMLVA NPIAAGRMPI QPFNAADFGQ AGQT AAAVA LAQAMFV |
-Macromolecule #5: VP1
Macromolecule | Name: VP1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Grass carp reovirus |
Molecular weight | Theoretical: 141.512156 KDa |
Recombinant expression | Organism: Ctenopharyngodon idella (grass carp) |
Sequence | String: MAAVFGIQLV PKLNTSTTRR TFLPLRFDLL LDRLQSTNLH GVLYRALDFN PVDRSATVIQ TYPPLNAWSP HHAFIENPLD YRDWTEFIH DRALAFVGVL TQRYPLTQNA QRYTNPLVLG AAFGDFLNAR SIDIFLDRLF YDPTQDSPIT AITKFPYQWT I DSNVTTDS ...String: MAAVFGIQLV PKLNTSTTRR TFLPLRFDLL LDRLQSTNLH GVLYRALDFN PVDRSATVIQ TYPPLNAWSP HHAFIENPLD YRDWTEFIH DRALAFVGVL TQRYPLTQNA QRYTNPLVLG AAFGDFLNAR SIDIFLDRLF YDPTQDSPIT AITKFPYQWT I DSNVTTDS VRTSAGCKYI TLYGYDPSRP STPATYGKHR PTYATVFYYS TLPARSRLLA NLAAGPTVLE HFDSPTYGPH LL LPQTGDV LGYSSSLISQ AALLMVESVM DALRDNANAS ASTAVTRLDQ SYHPVTSFDP STFNTLLQRA TNLALLAVQG VQS ESAIPA IPTMSDVRSF VARLMAEGDP QQWFPYRVDQ ILYWPESPFV PPIGPFYAPF RPVNFPFTTG SYTVVPDASR PLRL LPQYR NATITVQQAD DAYEDTALSP LITTHGFCVT GGVFTSIYDI SGDPTAYPPA QLVDAPNDYF DRERMARRDL FRRLR APAD RSAIKDRAVF DFLASLVNPT TANPVLDTSF SMAYLGASSA HANADEPVIL ADIRSGSIPG LPIPRRIVQF GYDVVH GSL LDLSRAVPTG TFGLVYADLD QVEDAGTDMP AANRAAIAML GTALQMTTAG GVSVLKVNFP TRAFWTQVFN LYATHAT TL HLVKPTIVNS SEVFLVFGGR QSNGALRSTT ALQRALLSLY ARNAAIDRAV THIPFFGVPD DGTSDLGIDA VRLFDPMF S DAVANLPSNA LASLVSRVVP SSIMFTRVPS NGPVSTTIYG KRTFLSNRRR ARLRDVPMLI TTTLVHQRRF TTPPTFTLF SSEAVPVTTL VAAGYNSFIS EQTRNPNLAH LLDLGTGPEC RILSLIPPTL QVTMSDSRPC AELMASFDPA LTAYVQGDYS TAAFWNGIR CDSATAIFTI GAAAAAAGTD LIAFVQQLIP RIVAAGGTRM WLQLNTPLYE VSSLPDLIEI DLRDHVYRFN G GERVEPYA DPVPLQQAIA ALLPAAALSW HTLSPTCDWL PYIIGVGSPL NLSDINTAIS YSRLTPILHI DTTTPPLRVN PV PTPLNQQ CAIRITSLDP AAVLSVQHNG VEVIGGTPGN VISVAGAAAL QYILANQEFL LQFTPTLPGI FDVFLTTLGQ PPV PRGSFT ITPPPTTVAL NMPPPRQLDF TDVGNDARIT CDPYYQLAVC IFKDGQYVRV NPEKASVVTN APNRDLHFVL DLAD NHVLL YLCDVTPSGL GDRIAFPIVD IYRIAFPRNT PVRASLPYTG GGAHLTSGGN PFMSLTTPPA VLPAGVALAA LSTSV ATQY PTYTLPAGVY EYVIE |
-Macromolecule #6: VP3
Macromolecule | Name: VP3 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Grass carp reovirus |
Molecular weight | Theoretical: 132.203312 KDa |
Recombinant expression | Organism: Ctenopharyngodon idella (grass carp) |
Sequence | String: 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 |
-Macromolecule #7: MYRISTIC ACID
Macromolecule | Name: MYRISTIC ACID / type: ligand / ID: 7 / Number of copies: 10 / Formula: MYR |
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Molecular weight | Theoretical: 228.371 Da |
Chemical component information | ChemComp-MYR: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41000 |
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Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |