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- PDB-8rbs: Emiliania huxleyi virus 201 (EhV-201) asymmetrical unit of capsid... -

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Basic information

Entry
Database: PDB / ID: 8rbs
TitleEmiliania huxleyi virus 201 (EhV-201) asymmetrical unit of capsid proteins predicted by AlphaFold2 fitted into the cryo-EM density of EhV-201 virion composite map.
Components
  • Major capsid protein
  • Penton protein
KeywordsVIRUS / cryo-EM / subtomogram averaging / EhV-201 / enveloped virus / capsid / major capsid protein / composite map
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
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 18 Å
AuthorsHomola, M. / Buttner, C.R. / Fuzik, T. / Novacek, J. / Chaillet, M. / Forster, F. / Plevka, P.
Funding support Czech Republic, European Union, 2items
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, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionDec 20, 2023ID: 8PFN
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: Major capsid protein
A2: Major capsid protein
A3: Major capsid protein
A4: Major capsid protein
A5: Major capsid protein
A6: Major capsid protein
A7: Major capsid protein
A8: Major capsid protein
A9: Major capsid protein
B1: Major capsid protein
B2: Major capsid protein
B3: Major capsid protein
B4: Major capsid protein
B5: Major capsid protein
B6: Major capsid protein
B7: Major capsid protein
B8: Major capsid protein
B9: Major capsid protein
C1: Major capsid protein
C2: Major capsid protein
C3: Major capsid protein
C4: Major capsid protein
C5: Major capsid protein
C6: Major capsid protein
C7: Major capsid protein
C8: Major capsid protein
C9: Major capsid protein
D1: Major capsid protein
D2: Major capsid protein
D3: Major capsid protein
D4: Major capsid protein
D5: Major capsid protein
D6: Major capsid protein
D7: Major capsid protein
D8: Major capsid protein
D9: Major capsid protein
E1: Major capsid protein
E2: Major capsid protein
E3: Major capsid protein
E4: Major capsid protein
E5: Major capsid protein
E6: Major capsid protein
E7: Major capsid protein
E8: Major capsid protein
E9: Major capsid protein
F1: Major capsid protein
F2: Major capsid protein
F3: Major capsid protein
F4: Major capsid protein
F5: Major capsid protein
F6: Major capsid protein
F7: Major capsid protein
F8: Major capsid protein
F9: Major capsid protein
G1: Major capsid protein
G2: Major capsid protein
G3: Major capsid protein
G4: Major capsid protein
G5: Major capsid protein
G6: Major capsid protein
G7: Major capsid protein
G8: Major capsid protein
G9: Major capsid protein
H1: Major capsid protein
H2: Major capsid protein
H3: Major capsid protein
H4: Major capsid protein
H5: Major capsid protein
H6: Major capsid protein
H7: Major capsid protein
H8: Major capsid protein
H9: Major capsid protein
I1: Major capsid protein
I2: Major capsid protein
I3: Major capsid protein
I4: Major capsid protein
I5: Major capsid protein
I6: Major capsid protein
I7: Major capsid protein
I8: Major capsid protein
I9: Major capsid protein
J1: Major capsid protein
J2: Major capsid protein
J3: Major capsid protein
K: Penton protein


Theoretical massNumber of molelcules
Total (without water)4,705,08685
Polymers4,705,08685
Non-polymers00
Water0
1
A1: Major capsid protein
A2: Major capsid protein
A3: Major capsid protein
A4: Major capsid protein
A5: Major capsid protein
A6: Major capsid protein
A7: Major capsid protein
A8: Major capsid protein
A9: Major capsid protein
B1: Major capsid protein
B2: Major capsid protein
B3: Major capsid protein
B4: Major capsid protein
B5: Major capsid protein
B6: Major capsid protein
B7: Major capsid protein
B8: Major capsid protein
B9: Major capsid protein
C1: Major capsid protein
C2: Major capsid protein
C3: Major capsid protein
C4: Major capsid protein
C5: Major capsid protein
C6: Major capsid protein
C7: Major capsid protein
C8: Major capsid protein
C9: Major capsid protein
D1: Major capsid protein
D2: Major capsid protein
D3: Major capsid protein
D4: Major capsid protein
D5: Major capsid protein
D6: Major capsid protein
D7: Major capsid protein
D8: Major capsid protein
D9: Major capsid protein
E1: Major capsid protein
E2: Major capsid protein
E3: Major capsid protein
E4: Major capsid protein
E5: Major capsid protein
E6: Major capsid protein
E7: Major capsid protein
E8: Major capsid protein
E9: Major capsid protein
F1: Major capsid protein
F2: Major capsid protein
F3: Major capsid protein
F4: Major capsid protein
F5: Major capsid protein
F6: Major capsid protein
F7: Major capsid protein
F8: Major capsid protein
F9: Major capsid protein
G1: Major capsid protein
G2: Major capsid protein
G3: Major capsid protein
G4: Major capsid protein
G5: Major capsid protein
G6: Major capsid protein
G7: Major capsid protein
G8: Major capsid protein
G9: Major capsid protein
H1: Major capsid protein
H2: Major capsid protein
H3: Major capsid protein
H4: Major capsid protein
H5: Major capsid protein
H6: Major capsid protein
H7: Major capsid protein
H8: Major capsid protein
H9: Major capsid protein
I1: Major capsid protein
I2: Major capsid protein
I3: Major capsid protein
I4: Major capsid protein
I5: Major capsid protein
I6: Major capsid protein
I7: Major capsid protein
I8: Major capsid protein
I9: Major capsid protein
J1: Major capsid protein
J2: Major capsid protein
J3: Major capsid protein
K: Penton protein
x 60


  • defined by author&software
  • Evidence: electron microscopy, not applicable
  • 282 MDa, 5100 polymers
Theoretical massNumber of molelcules
Total (without water)282,305,1575100
Polymers282,305,1575100
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein ...
Major capsid protein


Mass: 55145.770 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Details: AlphaFold2 predicted structure. / Source: (natural) Emiliania huxleyi virus 201 / References: UniProt: G9E4T6
#2: Protein Penton protein /


Mass: 72841.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: AlphaFold2 predicted structure. / Source: (natural) Emiliania huxleyi virus 201 / References: UniProt: Q4A2T2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Emiliania huxleyi virus 201 / Type: VIRUS
Details: EhV-201 was propagated on a non-calcifying Emiliania huxleyi strain (CCPM 2090).
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Emiliania huxleyi virus 201
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Emiliania huxleyi CCMP1516 / Strain: CCMP 2090
Virus shell
IDEntity assembly-IDNameDiameter (nm)Triangulation number (T number)
11inner membrane
21capsid1990169
31outer membrane2110
Buffer solutionpH: 8
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.
Buffer componentUnits: 40 / Name: sea salt
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The viral sample was concentrated down to 1x10^10 plaque-forming units per ml (PFU ml^-1)
Specimen supportDetails: top side only / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K
Details: Sample: 3.5 ul; Wait time: 10 s; Blot time: 3 s; Blot force: -2; Drain time: 0 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 42000 X / Calibrated magnification: 42000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Calibrated defocus min: 2000 nm / Calibrated defocus max: 4000 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 77 K
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 2.42 e/Å2 / Avg electron dose per subtomogram: 80 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 4323
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV
Image scansSampling size: 5 µm / Width: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1emClarity1.5.3.11volume selection
2Warp1.0.9volume selection
3SerialEM4image acquisition
5Warp1.0.9CTF correction
8UCSF ChimeraX1.5model fitting
11RELION4final Euler assignment
12RELION4classification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3152 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
EM volume selectionMethod: template matching / Num. of tomograms: 131 / Num. of volumes extracted: 10240
Reference model: EhV-201 virion vertex reconstruction coming out of localized single particle reconstruction
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model building
ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11G9E4T61AlphaFoldin silico model
21Q4A2T22AlphaFoldin silico model

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