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Yorodumi- EMDB-32508: Detached spike from Bombyx mori cytoplasmic polyhedrosis virus pa... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32508 | |||||||||||||||||||||||||||||||||
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Title | Detached spike from Bombyx mori cytoplasmic polyhedrosis virus particle | |||||||||||||||||||||||||||||||||
Map data | ||||||||||||||||||||||||||||||||||
Sample |
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Keywords | Cell attachment / Membrane penetration / VIRAL PROTEIN | |||||||||||||||||||||||||||||||||
Function / homology | PPPDE peptidase domain / PPPDE domain profile. / peptidase activity / PPPDE domain-containing protein Function and homology information | |||||||||||||||||||||||||||||||||
Biological species | Bombyx mori cypovirus 1 | |||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||||||||||||||||||||||||||
Authors | Zhang Y / Cui Y / Sun J / Zhou ZH | |||||||||||||||||||||||||||||||||
Funding support | United States, 10 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Multiple conformations of trimeric spikes visualized on a non-enveloped virus. Authors: Yinong Zhang / Yanxiang Cui / Jingchen Sun / Z Hong Zhou / Abstract: Many viruses utilize trimeric spikes to gain entry into host cells. However, without in situ structures of these trimeric spikes, a full understanding of this dynamic and essential process of viral ...Many viruses utilize trimeric spikes to gain entry into host cells. However, without in situ structures of these trimeric spikes, a full understanding of this dynamic and essential process of viral infections is not possible. Here we present four in situ and one isolated cryoEM structures of the trimeric spike of the cytoplasmic polyhedrosis virus, a member of the non-enveloped Reoviridae family and a virus historically used as a model in the discoveries of RNA transcription and capping. These structures adopt two drastically different conformations, closed spike and opened spike, which respectively represent the penetration-inactive and penetration-active states. Each spike monomer has four domains: N-terminal, body, claw, and C-terminal. From closed to opened state, the RGD motif-containing C-terminal domain is freed to bind integrins, and the claw domain rotates to expose and project its membrane insertion loops into the cellular membrane. Comparison between turret vertices before and after detachment of the trimeric spike shows that the trimeric spike anchors its N-terminal domain in the iris of the pentameric RNA-capping turret. Sensing of cytosolic S-adenosylmethionine (SAM) and adenosine triphosphate (ATP) by the turret triggers a cascade of events: opening of the iris, detachment of the spike, and initiation of endogenous transcription. | |||||||||||||||||||||||||||||||||
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_32508.map.gz | 117.1 MB | EMDB map data format | |
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Header (meta data) | emd-32508-v30.xml emd-32508.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
Images | emd_32508.png | 76.7 KB | ||
Filedesc metadata | emd-32508.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32508 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32508 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32508.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.062 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Bombyx mori cypovirus 1
Entire | Name: Bombyx mori cypovirus 1 |
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Components |
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-Supramolecule #1: Bombyx mori cypovirus 1
Supramolecule | Name: Bombyx mori cypovirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 110829 / Sci species name: Bombyx mori cypovirus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Bombyx mori (domestic silkworm) |
-Macromolecule #1: Spike protein encoded by S3 gene of the Bombyx mori cytoplasmic p...
Macromolecule | Name: Spike protein encoded by S3 gene of the Bombyx mori cytoplasmic polyhedrosis virus. type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bombyx mori cypovirus 1 |
Sequence | String: MEINRAEIRR EITRYTGLIE QQTQLNISDN DENILKTLIA DYNLRMRRDA LLGELARLDE LRDISQVKGV EYKVTIPLL PVISTLNQHE FEITQANIET DFIADNVTFV TSFVPADLDL EQTIQRVFFR TTATTPHFQS F NLVIEILN YDQDSGDVEL HVKIMIVRPN ...String: MEINRAEIRR EITRYTGLIE QQTQLNISDN DENILKTLIA DYNLRMRRDA LLGELARLDE LRDISQVKGV EYKVTIPLL PVISTLNQHE FEITQANIET DFIADNVTFV TSFVPADLDL EQTIQRVFFR TTATTPHFQS F NLVIEILN YDQDSGDVEL HVKIMIVRPN SDVVNYDYTW IGKDYERISV CYNLISHLQR IDGPHGRDDE AE MPIYRII RRDSGSIPSY ASGEHLYVIS SHLHVDEIVR RREHKSISVD VTQLSLILPI IRTFNPVDLR EVR IEDITP GIEFTINMEV STYLAESSGS HVDMQRAIMN HADKIVGNYT GQQWNVQSNM LSEVRTQMLE EEDE EARQR GDYTTSTLVQ TMAQVSDLFS STILYRRAEA RLDNTVGAFE LLRPVLSIPS EYVHNGRVGP ITNIP ANAS IVTSSSSGAG QVRNIFKPIG DQTINESHFA NVFSNDEYAI YLRFSYRQAP VQSETVYLQQ NLPSMR IVS PSSVSTTVST AVIGGNTIHI NCPIRPHRED RLVSGGVQVP RQSTAVEIRV QEILIGYRQA TTFPIDT EG RLSLELMYGL ESRSAVGNTM SPVRFVTVND GEFFGLTCPI DLTLSTVVDP SSYLSDGVIL VATAFEDL R GYAWVATLGG DWPRTYNSSM RAFNVLTGGD INLSTEYGSE MTYTFKVELP IVYMFNNMTV ISNNVPRVP VLGVTYASIY QDSRTELEAR RFLQTLVFRI HGNWSARIPY TPGNLPTRNT ANQHQDIQQV INDSISQELG RLSDELLNM KNRLDHLERQ FEMFIQSQES EWWEILLNVV MDTVLGYFST FAGNALKSAQ QAISKAVGYT R RVLMTVTK TMRNGPIFTR LLGAKNLSGQ ALASLETLVE SVLRSINVKK SRFMSGAEPL YKNNKVAQHI DN TEKMNMM MDFSFANRNN RQNITADTLS RMHTQNAHGT SDTVLPAMRV YYRPLGFLDK RVGEALHKGI TRP EALKKQ LRSDVANVGT RAPSHAFMTY TDVLYEDAGS YIVSKRYLGI GELNRFGRTT SDKNADIGGV NIKY RVNKI TADGKYIIDR LSHTESGYTA ADVDRLYRSL FGKQGDGLST EQKWMDISRG VDAKIISADM VSEEF LSSK YTGQMIDELI NSPPQFNYSL IYRNCQDFVL DVLRVAQGFS PSNKWDVSTA ARMQQRRVIS LMDDLM SES ETFARSAHSN HSLLQQIRRS YVKARKRGDL HTVKALQLRL KGFFQI |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69035 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |