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- EMDB-0174: Cryo-EM structure of archaeal extremophilic internal membrane-con... -

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Entry
Database: EMDB / ID: EMD-0174
TitleCryo-EM structure of archaeal extremophilic internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) at 3.74 Angstroms resolution.
Map dataCentered map 0 0 0
Sample
  • Virus: Haloarcula californiae icosahedral virus 1
    • Protein or peptide: VP7
    • Protein or peptide: VP9
    • Protein or peptide: GPS-III molecule located underneath the capsomer close to the icosahedral three-fold axis.
    • Protein or peptide: GPS-II protein located underneath the two-tower capsomer NOT sitting on the icosahedral 2-fold axis.
    • Protein or peptide: (Half) GPS-II protein located underneath the two-tower capsomer sitting ON the icosahedral 2-fold axis.
    • Protein or peptide: Peripentonal unknown polypeptide
    • Protein or peptide: VP4
Function / homologyVP7 / VP4 / VP9
Function and homology information
Biological speciesHaloarcula californiae ATCC 33799 (Halophile) / Haloarcula californiae icosahedral virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsAbrescia NG / Santos-Perez I / Charro D
Funding support Spain, Finland, 4 items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2015-64541-R Spain
Spanish Ministry of Economy and CompetitivenessSEV-2016-0644 Spain
Academy of Finland1306833, 255342,256518,283072 Finland
Other governmentBasque Governament PRE_2016_2_0151 Spain
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for assembly of vertical single β-barrel viruses.
Authors: Isaac Santos-Pérez / Diego Charro / David Gil-Carton / Mikel Azkargorta / Felix Elortza / Dennis H Bamford / Hanna M Oksanen / Nicola G A Abrescia /
Abstract: The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The ...The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The discovery of PRD1-like viruses with two MCPs challenged the known assembly principles. Here, we present the cryo-electron microscopy (cryo-EM) structures of the archaeal, halophilic, internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) and Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.7 and 3.8 Å resolution, respectively. Our structures reveal proteins located beneath the morphologically distinct two- and three-tower capsomers and homopentameric membrane proteins at the vertices that orchestrate the positioning of pre-formed vertical single β-barrel MCP heterodimers. The cryo-EM based structures together with the proteomics data provide insights into the assembly mechanism of this type of viruses and into those with membrane-less double β-barrel MCPs.
History
DepositionAug 3, 2018-
Header (metadata) releaseMar 27, 2019-
Map releaseMar 27, 2019-
UpdateDec 14, 2022-
Current statusDec 14, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6h9c
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6h9c
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0174.png

Downloads & links

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Map

FileDownload / File: emd_0174.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCentered map 0 0 0
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.059673354 - 0.13143641
Average (Standard dev.)0.00030218353 (±0.008050988)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-383-383-383
Dimensions768768768
Spacing768768768
CellA=B=C: 1075.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z768768768
origin x/y/z0.0000.0000.000
length x/y/z1075.2001075.2001075.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S312
start NC/NR/NS-383-383-383
NC/NR/NS768768768
D min/max/mean-0.0600.1310.000

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Supplemental data

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Mask #1

Fileemd_0174_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_0174_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: None

Fileemd_0174_half_map_1.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: None

Fileemd_0174_half_map_2.map
AnnotationNone
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Haloarcula californiae icosahedral virus 1

EntireName: Haloarcula californiae icosahedral virus 1
Components
  • Virus: Haloarcula californiae icosahedral virus 1
    • Protein or peptide: VP7
    • Protein or peptide: VP9
    • Protein or peptide: GPS-III molecule located underneath the capsomer close to the icosahedral three-fold axis.
    • Protein or peptide: GPS-II protein located underneath the two-tower capsomer NOT sitting on the icosahedral 2-fold axis.
    • Protein or peptide: (Half) GPS-II protein located underneath the two-tower capsomer sitting ON the icosahedral 2-fold axis.
    • Protein or peptide: Peripentonal unknown polypeptide
    • Protein or peptide: VP4

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Supramolecule #1: Haloarcula californiae icosahedral virus 1

SupramoleculeName: Haloarcula californiae icosahedral virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Haloarcula californiae icosahedral virus - 1 / NCBI-ID: 662475
Sci species name: Haloarcula californiae icosahedral virus 1
Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Haloarcula californiae ATCC 33799 (Halophile)
Virus shellShell ID: 1 / Diameter: 800.0 Å / T number (triangulation number): 28

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Macromolecule #1: VP7

MacromoleculeName: VP7 / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula californiae ATCC 33799 (Halophile)
Molecular weightTheoretical: 19.912832 KDa
SequenceString:
MGNIGNLSAE KQISLYDGQP FISEQDVAAG DPNTPALTIE GPDGYVIAVD AGTPIAPEFR DSNGEKLDPS TRVIVQKCDR QGNPLGDGI IFNDTLGRFN YNKMRTDPDY MRKTAKSLMV DEREIVKVFV DVPDGANGYD AERSRFTLGD DTSDFGKAVE I VDHDDLTE GETQAVKSAS QRSGGA

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Macromolecule #2: VP9

MacromoleculeName: VP9 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula californiae ATCC 33799 (Halophile)
Molecular weightTheoretical: 16.271062 KDa
SequenceString:
MRDNQDLLVK RLGRLVNVLE SKEFGGTTTV DKDLDVTKNV TRTDEPNEDN TPDYFSTGKD RVLVPDTEEW ERLGFGIVAK TVNVRTTDD VLLAFANPNT NGPTFKIRSN ESPFTIGGDA GIDTAFMWLK KAESAQNDPA VEIIAYR

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Macromolecule #3: GPS-III molecule located underneath the capsomer close to the ico...

MacromoleculeName: GPS-III molecule located underneath the capsomer close to the icosahedral three-fold axis.
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula californiae ATCC 33799 (Halophile)
Molecular weightTheoretical: 9.209344 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

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Macromolecule #4: GPS-II protein located underneath the two-tower capsomer NOT sitt...

MacromoleculeName: GPS-II protein located underneath the two-tower capsomer NOT sitting on the icosahedral 2-fold axis.
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula californiae ATCC 33799 (Halophile)
Molecular weightTheoretical: 6.400881 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #5: (Half) GPS-II protein located underneath the two-tower capsomer s...

MacromoleculeName: (Half) GPS-II protein located underneath the two-tower capsomer sitting ON the icosahedral 2-fold axis.
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula californiae ATCC 33799 (Halophile)
Molecular weightTheoretical: 3.932839 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #6: Peripentonal unknown polypeptide

MacromoleculeName: Peripentonal unknown polypeptide / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula californiae ATCC 33799 (Halophile)
Molecular weightTheoretical: 1.549902 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #7: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 7 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula californiae ATCC 33799 (Halophile)
Molecular weightTheoretical: 25.995318 KDa
SequenceString: MADQTQEYTL SHTGGLLGSS KVTTASNQTA PQRETAIISF EVPRKFSEIE YVGQRDATRF VPRTTEEITG TANDDTVVQL QANIQPIAG EEDMADQDYP VVVAYNVTQG AQVEIADVNY ATDEVTLATD PADGDTVKLW PIMGDGEVQF RLVNQFGQEE G RVYPWATP ...String:
MADQTQEYTL SHTGGLLGSS KVTTASNQTA PQRETAIISF EVPRKFSEIE YVGQRDATRF VPRTTEEITG TANDDTVVQL QANIQPIAG EEDMADQDYP VVVAYNVTQG AQVEIADVNY ATDEVTLATD PADGDTVKLW PIMGDGEVQF RLVNQFGQEE G RVYPWATP LYRWHDFPQL KRGREINLHG SVTWQENETV EVLLDAPQAI TWEDADYPEG QYVSTFEQDV EITL

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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

Concentration1.2 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
1.0 MNaClSodium chlorideSodium Chloride
70.0 mMMgCl2Magnesium Chloride
20.0 mMKClPotasium Chloride
1.0 mMCaCl2Calcium Chloride
50.0 mMC4H11NO3Tris-HClTris
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III
DetailsHaloarcula californiae icosahedral virus 1. Taxonomic identifier 1735722 NCBI.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.9 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-26 / Number grids imaged: 1 / Number real images: 3218 / Average electron dose: 36.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4584
Startup modelType of model: OTHER
Details: Associate ENTRY (HHIV-2 at 4.4 Angstroms resolution).
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 10 / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 3414
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsThe HCIV-1 VP7 and VP4 MCPs were manually built aided by beta-barrel core templates derived from the crystal structures of Thermus bacteriophage P23-77 MCPs (PDB ID 3ZN6).
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 89.1 / Target criteria: Cross-correlation coefficient
Output model

PDB-6h9c:
Cryo-EM structure of archaeal extremophilic internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) at 3.74 Angstroms resolution.

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