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- EMDB-32506: 5-fold vertex of Bombyx mori cytoplasmic polyhedrosis virus forme... -

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Basic information

Entry
Database: EMDB / ID: EMD-32506
Title5-fold vertex of Bombyx mori cytoplasmic polyhedrosis virus formed by trimeric spike and pentameric turret
Map data
Sample
  • Virus: Bombyx mori cypovirus 1
    • Protein or peptide: Spike protein encoded by S3 gene of Bombyx mori cytoplasmic polyhedrosis virus.
    • Protein or peptide: Turret protein encoded by S4 gene of Bombyx mori cytoplasmic polyhedrosis virus
KeywordsComplex / Cell attachment / Membrane penetration / Capping enzyme / VIRAL PROTEIN
Function / homology
Function and homology information


PPPDE peptidase domain / PPPDE domain profile. / : / : / : / : / Reovirus VP3 protein, guanylyltransferase (GTase) / Reovirus turret protein, bridge domain / Reovirus VP3 protein, Methyltransferase domain 1 / Reovirus VP3 protein, Methyltransferase domain 2
Similarity search - Domain/homology
PPPDE domain-containing protein / Structural protein VP3
Similarity search - Component
Biological speciesBombyx mori cypovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsZhang Y / Cui Y / Sun J / Zhou ZH
Funding support China, 10 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31672489 China
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028583 China
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE025567 China
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 China
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1S10RR23057 China
National Institutes of Health/Office of the Director1S10OD018111 China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 China
National Science Foundation (NSF, United States)DMR-1548924 China
National Science Foundation (NSF, United States)DBI-1338135 China
CitationJournal: 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
DepositionDec 31, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32506.png

Downloads & links

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Map

FileDownload / File: emd_32506.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.)
1.06 Å/pix.
x 320 pix.
= 339.84 Å		1.06 Å/pix.
x 320 pix.
= 339.84 Å		1.06 Å/pix.
x 320 pix.
= 339.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.062 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.016027953 - 0.022913296
Average (Standard dev.)-0.00003282984 (±0.001433273)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.84003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0621.0621.062
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z339.840339.840339.840
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0160.023-0.000

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Supplemental data

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Sample components

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Entire : Bombyx mori cypovirus 1

EntireName: Bombyx mori cypovirus 1
Components
  • Virus: Bombyx mori cypovirus 1
    • Protein or peptide: Spike protein encoded by S3 gene of Bombyx mori cytoplasmic polyhedrosis virus.
    • Protein or peptide: Turret protein encoded by S4 gene of Bombyx mori cytoplasmic polyhedrosis virus

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Supramolecule #1: Bombyx mori cypovirus 1

SupramoleculeName: 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
Host (natural)Organism: Bombyx mori (domestic silkworm)

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Macromolecule #1: Spike protein encoded by S3 gene of Bombyx mori cytoplasmic polyh...

MacromoleculeName: Spike protein encoded by S3 gene of Bombyx mori cytoplasmic polyhedrosis virus.
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori cypovirus 1
SequenceString: 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

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Macromolecule #2: Turret protein encoded by S4 gene of Bombyx mori cytoplasmic poly...

MacromoleculeName: Turret protein encoded by S4 gene of Bombyx mori cytoplasmic polyhedrosis virus
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori cypovirus 1
SequenceString: MWHYTSINND TRVALDPKPN QIRTITKPNT VPQLGTDYLY TFNSQRRSHT LRLLGPFQYF NFSETDRGHP LFRLPLKYPS KAIPADELI DNLHSWMRSV HLLHVRSEDN TLRYNWMLGV YARSTNYTTP VGQLVVNAPA ILNYSNPQDA FNSVFVALGI D YIDIPITN ...String:
MWHYTSINND TRVALDPKPN QIRTITKPNT VPQLGTDYLY TFNSQRRSHT LRLLGPFQYF NFSETDRGHP LFRLPLKYPS KAIPADELI DNLHSWMRSV HLLHVRSEDN TLRYNWMLGV YARSTNYTTP VGQLVVNAPA ILNYSNPQDA FNSVFVALGI D YIDIPITN SNIFDDSSTP YNVRIWHAPT MTEVNHILAL MRKSTLVSTH SSWHWNVLHT FHYRSESDMI DHFAAKILED WR QKEKLDK GALVEADRVI QRLIPLSSST YVQRLAAIGA LYPNEFTENV LDLSRLSTAL LQLSDTYYQH ANDQLRRLYR RMY NDSRTL YMTQRHQELL LAQITADPNI LLYPYTYIFT TIPTSMNYIS NTGQGRIKHS LTVTGATEHD TVADIVLGQT GEDV ITISM VEPMSIAVED MYGYVLDTPT RDIWPADEQI EQKGDAVALY DTKTSRALGM FNNTVRIDDL LSPLLSLVYR TYIKG DTMT MTQGSLDHLT LCAAVDSDIT FVGNRMIAPL PEGYIPKPMH RNNSTMKMLS LYVALKKLEN FATNSYLMAP DTSIIL LGA EREPAVNILR RFNRNVSNVR IIGMGDRAVE PNIRVRVPFP IDKNISADFI ICDINSYEDQ SFESMFSETI SVVTTCA SA ATRALVKINH PSEYMINSVI ERLSQLGGVF YHTALLKTAS QNPYSYETYI YITPIAAAVR FPFYSNSAMI NRYMTAVA D DEMPIIPSIH TVIKGHSNTY SPGLFCGCVD VQSAPLALSQ LKSYCSEATT WRVDSDDNLV NIIARIDPAR IALEFRTRS NTSAYHEYQR YVPNGLGFKV RKTREFRYMH REVTFIHKLM MYALIREQIS LTENMTQVVS IGGRNLADIS VVPLNMKYVV IDPATRIET LTQEKKNIEV QSRPFQFDAA NMDLENNSIY LFIAVIMNEP NGAATPARMQ MDKIRNVATA MLTRTNCVAY I SFYEAGII TRLDQSTAHK TIRVEEGRLK VANYVPVDTL VEADVTLMLR DIGITHEIIR PSTPELIDAC SNYGIRLGST GG AVLDVFN HYSPVIKLVR S

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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
Component:
ConcentrationFormulaName
70.0 mmol/L (mM)C4H12ClNO32-amino-2-(hydroxymethyl)propane-1,3-diol dihydrochloride (Tris-HCl)
100.0 mmol/L (mM)NaClSodium Chloride
10.0 mmol/L (mM)MgCl2Magnesium Chloride
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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: 2.3000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69955
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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