+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9050 | |||||||||||||||||||||||||||
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タイトル | In situ structure of transcriptional enzyme complex and asymmetric inner capsid protein of aquareovirus at primed state | |||||||||||||||||||||||||||
マップデータ | Grass Carp reovirus TEC structure at primed state | |||||||||||||||||||||||||||
試料 | transcriptional enzyme complex and asymmetric inner capsid protein != Grass carp reovirus transcriptional enzyme complex and asymmetric inner capsid protein
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機能・相同性 | 機能・相同性情報 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 類似検索 - 分子機能 | |||||||||||||||||||||||||||
生物種 | Grass carp reovirus (ウイルス) | |||||||||||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | |||||||||||||||||||||||||||
データ登録者 | Ding K / Zhou ZH | |||||||||||||||||||||||||||
資金援助 | 米国, 8件
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引用 | ジャーナル: J Virol / 年: 2018 タイトル: Structures of the Polymerase Complex and RNA Genome Show How Aquareovirus Transcription Machineries Respond to Uncoating. 著者: Ke Ding / Lisa Nguyen / Z Hong Zhou / 要旨: Reoviruses carry out genomic RNA transcription within intact viruses to synthesize plus-sense RNA strands, which are capped prior to their release as mRNA. The structures of the transcriptional ...Reoviruses carry out genomic RNA transcription within intact viruses to synthesize plus-sense RNA strands, which are capped prior to their release as mRNA. The structures of the transcriptional enzyme complex (TEC) containing the RNA-dependent RNA polymerase (RdRp) and NTPase are known for the single-layered reovirus cytoplasmic polyhedrosis virus (CPV), but not for multilayered reoviruses, such as aquareoviruses (ARV), which possess a primed stage that CPV lacks. Consequently, how the RNA genome and TEC respond to priming in reoviruses is unknown. Here, we determined the near-atomic-resolution asymmetric structure of ARV in the primed state by cryo-electron microscopy (cryo-EM), revealing the structures of 11 TECs inside each capsid and their interactions with the 11 surrounding double-stranded RNA (dsRNA) genome segments and with the 120 enclosing capsid shell protein (CSP) VP3 subunits. The RdRp VP2 and the NTPase VP4 associate with each other and with capsid vertices; both bind RNA in multiple locations, including a novel C-terminal domain of VP4. Structural comparison between the primed and quiescent states showed translocation of the dsRNA end from the NTPase to the RdRp during priming. The RNA template channel was open in both states, suggesting that channel blocking is not a regulating mechanism between these states in ARV. Instead, the NTPase C-terminal domain appears to regulate RNA translocation between the quiescent and primed states. Taking the data together, dsRNA viruses appear to have adapted divergent mechanisms to regulate genome transcription while retaining similar mechanisms to coassemble their genome segments, TEC, and capsid proteins into infectious virions. Viruses in the family are characterized by the ability to endogenously synthesize nascent RNA within the virus. However, the mechanisms for assembling their RNA genomes with transcriptional enzymes into a multilayered virion and for priming such a virion for transcription are poorly understood. By cryo-EM and novel asymmetric reconstruction, we determined the atomic structure of the transcription complex inside aquareoviruses (ARV) that are primed for infection. The transcription complex is anchored by the N-terminal segments of enclosing capsid proteins and contains an NTPase and a polymerase. The NTPase has a newly discovered domain that translocates the 5' end of plus-sense RNA in segmented dsRNA genomes from the NTPase to polymerase VP2 when the virus changes from the inactive (quiescent) to the primed state. Conformation changes in capsid proteins and transcriptional complexes suggest a mechanism for relaying information from the outside to the inside of the virus during priming. | |||||||||||||||||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_9050.map.gz | 95.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9050-v30.xml emd-9050.xml | 18.6 KB 18.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_9050.png | 192.1 KB | ||
その他 | emd_9050_additional.map.gz | 1.1 GB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9050 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9050 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_9050_validation.pdf.gz | 734.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_9050_full_validation.pdf.gz | 733.8 KB | 表示 | |
XML形式データ | emd_9050_validation.xml.gz | 6.6 KB | 表示 | |
CIF形式データ | emd_9050_validation.cif.gz | 7.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9050 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9050 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_9050.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Grass Carp reovirus TEC structure at primed state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-追加マップ: True asymmetric reconstruction
ファイル | emd_9050_additional.map | ||||||||||||
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注釈 | True asymmetric reconstruction | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : transcriptional enzyme complex and asymmetric inner capsid protein
全体 | 名称: transcriptional enzyme complex and asymmetric inner capsid protein |
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要素 |
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-超分子 #1: Grass carp reovirus
超分子 | 名称: Grass carp reovirus / タイプ: virus / ID: 1 / 親要素: 0 / 含まれる分子: #1-#3 / NCBI-ID: 128987 / 生物種: Grass carp reovirus / ウイルスタイプ: VIRION / ウイルス・単離状態: STRAIN / ウイルス・エンベロープ: No / ウイルス・中空状態: No |
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宿主 | 生物種: Ctenopharyngodon idella (ソウギョ) |
-分子 #1: VP2
分子 | 名称: VP2 / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Grass carp reovirus (ウイルス) |
分子量 | 理論値: 141.685438 KDa |
配列 | 文字列: MEELFNALPQ PLQQLSLALA GEIPLTDHIF EQAASTWHVQ PRSLTYKLLD HIPFATPVVV PPSIYHSLDW SKCFAVNQDR VERIPTIDN PDDVYVPNSD IGPLLTSLHT IPDYGFLHPT IENDATTLRA ERARCASTFY KIASSQARQV KLDPIRMLGF L LLVQARPR ...文字列: 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 |
-分子 #2: Putative core protein NTPase/VP5
分子 | 名称: Putative core protein NTPase/VP5 / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Grass carp reovirus (ウイルス) |
分子量 | 理論値: 80.381516 KDa |
配列 | 文字列: MITIVVIPTA HFSWTDTNFL NSVDYRLTSQ PKIRDRFAVY APGWLRRQLD EFSASLTASE LLQALQTIPI PVKARCLLLP KPKRFAQWL LDVPSANIWH IPVTTLRATV ASKHPSSDVY NYIPDHVPPN AEFDTVTRRV AAGRDIYVRS TKVIGAPLCL A APAKYYAG ...文字列: 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 |
-分子 #3: VP3
分子 | 名称: VP3 / タイプ: protein_or_peptide / ID: 3 / コピー数: 10 / 光学異性体: LEVO |
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由来(天然) | 生物種: Grass carp reovirus (ウイルス) |
分子量 | 理論値: 132.203312 KDa |
配列 | 文字列: MPRRSARKAQ SAIASPADTN VVPAKDAPTT NSPPSTTSPN QAAADANQQQ AGIVSSQSGP NAVGDSAPSS SVNNDGDIIT RPTSDSIAA VANATKPAAV VSDPQSMKVT PIVNPSSYVC NVCNARFSTM SALSEHLRSD HRDDASTLLA TPMINNAIRS F LTAWDDIR ...文字列: 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 |
-分子 #4: PHOSPHATE ION
分子 | 名称: PHOSPHATE ION / タイプ: ligand / ID: 4 / コピー数: 1 / 式: PO4 |
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分子量 | 理論値: 94.971 Da |
Chemical component information | ChemComp-PO4: |
-分子 #5: ZINC ION
分子 | 名称: ZINC ION / タイプ: ligand / ID: 5 / コピー数: 1 / 式: ZN |
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分子量 | 理論値: 65.409 Da |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.5 |
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 400 |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 25.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | アルゴリズム: FOURIER SPACE / 解像度のタイプ: BY AUTHOR / 解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 73472 |
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初期 角度割当 | タイプ: PROJECTION MATCHING |
最終 角度割当 | タイプ: PROJECTION MATCHING |