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- EMDB-32504: Closed spike of Bombyx mori cytoplasmic polyhedrosis virus -

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Basic information

Entry
Database: EMDB / ID: EMD-32504
TitleClosed spike of Bombyx mori cytoplasmic polyhedrosis virus
Map dataIn situ structure of the closed-spike with C3 symmetry (q-CPV).
Sample
  • Virus: Bombyx mori cypovirus 1
    • Protein or peptide: PPPDE domain-containing protein
KeywordsCell attachment / Membrane penetration / VIRAL PROTEIN
Function / homologyPPPDE peptidase domain / PPPDE domain profile. / peptidase activity / PPPDE domain-containing protein
Function and homology information
Biological speciesBombyx mori cypovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7whm
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7whm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32504.png

Downloads & links

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Map

FileDownload / File: emd_32504.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ structure of the closed-spike with C3 symmetry (q-CPV).
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: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.0768079 - 0.12766859
Average (Standard dev.)-0.000026255711 (±0.0035258164)
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-0.0770.128-0.000

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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: PPPDE domain-containing protein

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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: PPPDE domain-containing protein

MacromoleculeName: PPPDE domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori cypovirus 1
Molecular weightTheoretical: 140.37025 KDa
SequenceString: MEINRAEIRR EITRYTGLIE QQTQLNISDN DENILKTLIA DYNLRMRRDA LLGELARLDE LRDISQVKGV EYKVTIPLLP VISTLNQHE FEITQANIET DFIADNVTFV TSFVPADLDL EQTIQRVFFR TTATTPHFQS FNLVIEILNY DQDSGDVELH V KIMIVRPN ...String:
MEINRAEIRR EITRYTGLIE QQTQLNISDN DENILKTLIA DYNLRMRRDA LLGELARLDE LRDISQVKGV EYKVTIPLLP VISTLNQHE FEITQANIET DFIADNVTFV TSFVPADLDL EQTIQRVFFR TTATTPHFQS FNLVIEILNY DQDSGDVELH V KIMIVRPN SDVVNYDYTW IGKDYERISV CYNLISHLQR IDGPHGRDDE AEMPIYRIIR RDSGSIPSYA SGEHLYVISS HL HVDEIVR RREHKSISVD VTQLSLILPI IRTFNPVDLR EVRIEDITPG IEFTINMEVS TYLAESSGSH VDMQRAIMNH ADK IVGNYT GQQWNVQSNM LSEVRTQMLE EEDEEARQRG DYTTSTLVQT MAQVSDLFSS TILYRRAEAR LDNTVGAFEL LRPV LSIPS EYVHNGRVGP ITNIPANASI VTSSSSGAGQ VRNIFKPIGD QTINESHFAN VFSNDEYAIY LRFSYRQAPV QSETV YLQQ NLPSMRIVSP SSVSTTVSTA VIGGNTIHIN CPIRPHREDR LVSGGVQVPR QSTAVEIRVQ EILIGYRQAT TFPIDT EGR LSLELMYGLE SRSAVGNTMS PVRFVTVNDG EFFGLTCPID LTLSTVVDPS SYLSDGVILV ATAFEDLRGY AWVATLG GD WPRTYNSSMR AFNVLTGGDI NLSTEYGSEM TYTFKVELPI VYMFNNMTVI SNNVPRVPVL GVTYASIYQD SRTELEAR R FLQTLVFRIH GNWSARIPYT PGNLPTRNTA NQHQDIQQVI NDSISQELGR LSDELLNMKN RLDHLERQFE MFIQSQESE WWEILLNVVM DTVLGYFSTF AGNALKSAQQ AISKAVGYTR RVLMTVTKTM RNGPIFTRLL GAKNLSGQAL ASLETLVESV LRSINVKKS RFMSGAEPLY KNNKVAQHID NTEKMNMMMD FSFANRNNRQ NITADTLSRM HTQNAHGTSD TVLPAMRVYY R PLGFLDKR VGEALHKGIT RPEALKKQLR SDVANVGTRA PSHAFMTYTD VLYEDAGSYI VSKRYLGIGE LNRFGRTTSD KN ADIGGVN IKYRVNKITA DGKYIIDRLS HTESGYTAAD VDRLYRSLFG KQGDGLSTEQ KWMDISRGVD AKIISADMVS EEF LSSKYT GQMIDELINS PPQFNYSLIY RNCQDFVLDV LRVAQGFSPS NKWDVSTAAR MQQRRVISLM DDLMSESETF ARSA HSNHS LLQQIRRSYV KARKRGDLHT VKALQLRLKG FFQI

UniProtKB: PPPDE domain-containing protein

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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: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 310662
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7whm:
Closed spike of Bombyx mori cytoplasmic polyhedrosis virus

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