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- EMDB-32507: Pentameric turret of Bombyx mori cytoplasmic polyhedrosis virus a... -

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Basic information

Entry
Database: EMDB / ID: EMD-32507
TitlePentameric turret of Bombyx mori cytoplasmic polyhedrosis virus after spike detaches.
Map data
Sample
  • Virus: Bombyx mori cypovirus 1
    • Protein or peptide: Structural protein VP3
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsCapping enzyme / VIRAL PROTEIN
Function / homology: / : / : / : / Reovirus VP3 protein, guanylyltransferase (GTase) / Reovirus turret protein, bridge domain / Reovirus VP3 protein, Methyltransferase domain 1 / Reovirus VP3 protein, Methyltransferase domain 2 / Structural protein VP3
Function and homology information
Biological speciesBombyx mori cypovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhang Y / Cui Y
Funding support China, United States, 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 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1S10RR23057 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
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-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7whp
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7whp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32507.png

Downloads & links

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Map

FileDownload / File: emd_32507.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 318.6 Å		1.06 Å/pix.
x 300 pix.
= 318.6 Å		1.06 Å/pix.
x 300 pix.
= 318.6 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: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.07338638 - 0.1105349
Average (Standard dev.)0.00088669977 (±0.009892095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 318.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0621.0621.062
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z318.600318.600318.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0730.1110.001

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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: Structural protein VP3
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Bombyx mori cypovirus 1

SupramoleculeName: Bombyx mori cypovirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / 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: Structural protein VP3

MacromoleculeName: Structural protein VP3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori cypovirus 1
Molecular weightTheoretical: 120.145797 KDa
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

UniProtKB: Structural protein VP3

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Macromolecule #2: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 2 / Number of copies: 4 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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
1.0 mmol/L (mM)C15H22N6O5SS-adenosyl-L-methionine (SAM)
4.0 mmol/L (mM)C10H16N5O13P3Adenosine-5'-triphosphate (ATP)
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: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3152
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

Initial modelPDB ID:

3jb3


Chain - Chain ID: A / Chain - Residue range: 1-1057 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7whp:
Pentameric turret of Bombyx mori cytoplasmic polyhedrosis virus after spike detaches.

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