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- EMDB-19036: Cryo-EM structure of the Emiliania huxleyi virus 201 (EhV-201) vi... -

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Basic information

Entry
Database: EMDB / ID: EMD-19036
TitleCryo-EM structure of the Emiliania huxleyi virus 201 (EhV-201) virion vertex with a diameter of 50 nm and a mask applied on the capsid layer.
Map dataResult from postprocessing masked by tight mask to remove surrounding noise.
Sample
  • Virus: Emiliania huxleyi virus 201
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Penton protein
Keywordscryo-EM / subtomogram averaging / EhV-201 / enveloped virus / capsid / major capsid protein / VIRUS
Function / homology
Function and homology information


viral capsid / structural molecule activity
Similarity search - Function
Major capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Major capsid protein / Uncharacterized protein
Similarity search - Component
Biological speciesEmiliania huxleyi virus 201
Methodsubtomogram averaging / cryo EM / Resolution: 12.0 Å
AuthorsHomola M / Buttner CR / Fuzik T / Novacek J / Chaillet M / Forster F / Plevka P
Funding support Czech Republic, European Union, 2 items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGX19-25982X Czech Republic
European Research Council (ERC)101043454European Union
CitationJournal: Sci Adv / Year: 2024
Title: Structure and replication cycle of a virus infecting climate-modulating alga .
Authors: Miroslav Homola / Carina R Büttner / Tibor Füzik / Pavel Křepelka / Radka Holbová / Jiří Nováček / Marten L Chaillet / Jakub Žák / Danyil Grybchuk / Friedrich Förster / William H ...Authors: Miroslav Homola / Carina R Büttner / Tibor Füzik / Pavel Křepelka / Radka Holbová / Jiří Nováček / Marten L Chaillet / Jakub Žák / Danyil Grybchuk / Friedrich Förster / William H Wilson / Declan C Schroeder / Pavel Plevka /
Abstract: The globally distributed marine alga has cooling effect on the Earth's climate. The population density of is restricted by viruses, including virus 201 (EhV-201). Despite the impact of viruses ...The globally distributed marine alga has cooling effect on the Earth's climate. The population density of is restricted by viruses, including virus 201 (EhV-201). Despite the impact of viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect by using fivefold vertices to bind to and fuse the virus' inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum-derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from cells, which enables the continuous release of virions by exocytosis.
History
DepositionDec 4, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19036.png

Downloads & links

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Map

FileDownload / File: emd_19036.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationResult from postprocessing masked by tight mask to remove surrounding noise.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.16 Å/pix.
x 128 pix.
= 532.48 Å		4.16 Å/pix.
x 128 pix.
= 532.48 Å		4.16 Å/pix.
x 128 pix.
= 532.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.102316596 - 0.48665527
Average (Standard dev.)0.019942425 (±0.06785583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 532.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19036_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Result from postprocessing - masked.

Fileemd_19036_additional_1.map
AnnotationResult from postprocessing - masked.
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AxesZYX

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Density Histograms

Histogram

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Half map: halfMap 1

Fileemd_19036_half_map_1.map
AnnotationhalfMap_1
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: halfMap 2

Fileemd_19036_half_map_2.map
AnnotationhalfMap_2
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Emiliania huxleyi virus 201

EntireName: Emiliania huxleyi virus 201
Components
  • Virus: Emiliania huxleyi virus 201
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Penton protein

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Supramolecule #1: Emiliania huxleyi virus 201

SupramoleculeName: Emiliania huxleyi virus 201 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: EhV-201 was propagated on a non-calcifying Emiliania huxleyi strain (CCPM 2090).
NCBI-ID: 181210 / Sci species name: Emiliania huxleyi virus 201 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Emiliania huxleyi CCMP1516 (eukaryote) / Strain: CCMP 2090
Virus shellShell ID: 1 / Name: inner membrane
Virus shellShell ID: 2 / Name: capsid / Diameter: 1990.0 Å / T number (triangulation number): 169
Virus shellShell ID: 3 / Name: outer membrane / Diameter: 2110.0 Å

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Details: AlphaFold2 predicted structure. / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Emiliania huxleyi virus 201
Molecular weightTheoretical: 55.14577 KDa
SequenceString: MSGFGGGSSG AGSLTQLLAT GSMDAALTQN ATRTFWKSSY QKHSLFALES INQPFTTQVQ FGAESHITVN RQGDLLSWMY LKIVLPGLK VQNQADTVQP TQQSFASLDN DVAAQADVSH VLPYIEGAYT EASLNTKEQL IAEAKNSYEA AKYNAAPLPV A AQMQSTEM ...String:
MSGFGGGSSG AGSLTQLLAT GSMDAALTQN ATRTFWKSSY QKHSLFALES INQPFTTQVQ FGAESHITVN RQGDLLSWMY LKIVLPGLK VQNQADTVQP TQQSFASLDN DVAAQADVSH VLPYIEGAYT EASLNTKEQL IAEAKNSYEA AKYNAAPLPV A AQMQSTEM PDFDYAYWTE AIGFHLIKRA EFKVGGATID TIWSELLFAM EELMGRAGRR LTETIGRTLR RPTELMKASR QE QILYVPL PWYFTKHPSL AFPLVAATYH NIQLWVQWAQ LNSCIIKSRS NLVVLHAERN VPISDDHLRA SLECTYVHLE AAE RDALTA NAGTQLIVQH QAHLQQVSSN NVTARLNFNF PVLEFYYFLR RKANKDAGDH FNFSGIGGRD PVVSAELLFN NTAR VTQKP AVWWRAVQAL QFHSSAPLTN IYSYSFSLSP EDPITPSGSA NFSRLDSVEL ALTLQDDFGA AHDANSELFV FARSY NILK FTNGLAGLLY SN

UniProtKB: Major capsid protein

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Macromolecule #2: Penton protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 2 / Details: AlphaFold2 predicted structure. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Emiliania huxleyi virus 201
Molecular weightTheoretical: 72.841266 KDa
SequenceString: MPSIAFSGIS TKPGELEFHV PSVLSKHNRA GLLKSIDFPY SQRTIESSWN KLHYMESIRI TPESRSVSVL LTDKESGDRV EMLAMVPLT TNKIIEISTA TTDGTIILVT EEPHGFFAPG CFGKEVRNVI SSYKSIFPHG TPPFILIHGS NGSVQVDPAL F EYNDEYSV ...String:
MPSIAFSGIS TKPGELEFHV PSVLSKHNRA GLLKSIDFPY SQRTIESSWN KLHYMESIRI TPESRSVSVL LTDKESGDRV EMLAMVPLT TNKIIEISTA TTDGTIILVT EEPHGFFAPG CFGKEVRNVI SSYKSIFPHG TPPFILIHGS NGSVQVDPAL F EYNDEYSV KIKYTAIRTE FKLFGKGDHG WMVTPEFPTI SMLCQVITNA MNSAIIFNHD DPAARTRMYP GTCSNTHVIE SV SGDSLAK ALLGYDGVYA GWEEITIPAG MYCYGELDLS KMIAAKMNRW HIDRESSIIF RGVSGYTWNV TLPSGNYGTP EKL AHCIQH MMNMTAKNRK NPYCVRFTLN EGSSHRGKFV FVAAEPFDLL FGDDESIDPS ILGFEPVDHI GRNSYMSEND LGAP LMKPN CNVYDVDEIP GTHQIRIGRR TRLAVDGKIR GYSGGTLRLN TVNRTTGAPK CHGMNKGDVV TLTTVMPAPD GATGT KREG FTFRAKNKIM GVVVADENEN PDASSLHVSV PSMSWTLGIG SYITIDSQAA PISVALFDPG KNQFFRDSIG ASRLGF SNG VSTGQHGVVV SQCAVNLEPR TVDVSFIEGS MTSASTEMYN QNGKSLITQV PSDRSSGPVP QGMVRFNNAL QQFKLEF TN PDGSPYHFNH ASLSLLMEFD D

UniProtKB: Uncharacterized protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Component - Name: sea salt
Details: Sea salts (Sigma Aldrich - S9883) were dissolved in distilled water (40 g/L w/v), filtered through a 0.22 um filter, and pH adjusted to 8.
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 5e-05 kPa / Details: top side only
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV
Details: Sample: 3.5 ul; Wait time: 10 s; Blot time: 3 s; Blot force: -2; Drain time: 0 s.
DetailsThe viral sample was concentrated down to 1x10^10 plaque-forming units per ml (PFU ml^-1)

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 77.0 K / Max: 77.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 4323 / Average exposure time: 1.5 sec. / Average electron dose: 2.42 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 2.0 µm / Calibrated magnification: 42000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 42000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 2880
ExtractionNumber tomograms: 131 / Number images used: 10240
Reference model: EhV-201 virion vertex reconstruction coming out of localized single particle reconstruction
Method: template matching
Software: (Name: emClarity (ver. 1.5.3.11), Warp (ver. 1.0.9))
Final 3D classificationNumber classes: 2 / Avg.num./class: 1600 / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

e4t6

source_name: AlphaFold, initial_model_type: in silico model

a2t2

source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-8rbt:
Emiliania huxleyi virus 201 (EhV-201) capsid proteins predicted by AlphaFold2 fitted into a cryo-EM density map of the EhV-201 virion capsid.

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