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- EMDB-0172: Cryo-EM structure of the archaeal extremophilic internal membrane... -

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Entry
Database: EMDB / ID: EMD-0172
TitleCryo-EM structure of the archaeal extremophilic internal membrane containing Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.78 Angstroms resolution.
Map dataMap derived from RELION postprocessed map. The map was then centred at 0,0,0 and finally used for model refinement.
Sample
  • Virus: Haloarcula hispanica icosahedral virus 2
    • Protein or peptide: VP4
    • Protein or peptide: VP7
    • Protein or peptide: VP7
    • Protein or peptide: VP7
    • Protein or peptide: Uncharacterized protein
    • Protein or peptide: VP16 (vertex complex)
    • Protein or peptide: GPS III
    • Protein or peptide: polypeptide stretch (vertex complex)
Keywordssingle vertical beta-barrel virus / archaeal / membrane-containing / quasi-atomic resolution / VIRUS
Function / homologyVP7 / VP4 / Uncharacterized protein
Function and homology information
Biological speciesHaloarcula hispanica icosahedral virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsAbrescia NG / Santos-Perez I
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_151) Spain
CitationJournal: Structure / Year: 2015
Title: Insight into the Assembly of Viruses with Vertical Single β-barrel Major Capsid Proteins.
Authors: David Gil-Carton / Salla T Jaakkola / Diego Charro / Bibiana Peralta / Daniel Castaño-Díez / Hanna M Oksanen / Dennis H Bamford / Nicola G A Abrescia /
Abstract: Archaeal viruses constitute the least explored niche within the virosphere. Structure-based approaches have revealed close relationships between viruses infecting organisms from different domains of ...Archaeal viruses constitute the least explored niche within the virosphere. Structure-based approaches have revealed close relationships between viruses infecting organisms from different domains of life. Here, using biochemical and cryo-electron microscopy techniques, we solved the structure of euryarchaeal, halophilic, internal membrane-containing Haloarcula hispanica icosahedral virus 2 (HHIV-2). We show that the density of the two major capsid proteins (MCPs) recapitulates vertical single β-barrel proteins and that disulfide bridges stabilize the capsid. Below, ordered density is visible close to the membrane and at the five-fold vertices underneath the host-interacting vertex complex underpinning membrane-protein interactions. The HHIV-2 structure exemplifies the division of conserved architectural elements of a virion, such as the capsid, from those that evolve rapidly due to selective environmental pressure such as host-recognizing structures. We propose that in viruses with two vertical single β-barrel MCPs the vesicle is indispensable, and membrane-protein interactions serve as protein-railings for guiding the assembly.
History
DepositionAug 1, 2018-
Header (metadata) releaseOct 31, 2018-
Map releaseApr 3, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.067
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.067
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6h82
  • Surface level: 0.067
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6h82
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0172.png

Downloads & links

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Map

FileDownload / File: emd_0172.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap derived from RELION postprocessed map. The map was then centred at 0,0,0 and finally used for model refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
1.34 Å/pix.
x 760 pix.
= 1018.4 Å		1.34 Å/pix.
x 760 pix.
= 1018.4 Å		1.34 Å/pix.
x 760 pix.
= 1018.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.067 / Movie #1: 0.067
Minimum - Maximum-0.05590476 - 0.16694117
Average (Standard dev.)0.009740791 (±0.015073328)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-379-379-379
Dimensions760760760
Spacing760760760
CellA=B=C: 1018.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z760760760
origin x/y/z0.0000.0000.000
length x/y/z1018.4001018.4001018.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-379-379-379
NX/NY/NZ760760760
MAP C/R/S312
start NC/NR/NS-379-379-379
NC/NR/NS760760760
D min/max/mean-0.0560.1670.010

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Supplemental data

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Mask #1

Fileemd_0172_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Relion post-processed map bfactor -40

Fileemd_0172_additional.map
AnnotationRelion post-processed map bfactor -40
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half maps for gold-standard FSC and generation of...

Fileemd_0172_half_map_1.map
AnnotationHalf maps for gold-standard FSC and generation of both submitted postprocessed maps.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_0172_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Haloarcula hispanica icosahedral virus 2

EntireName: Haloarcula hispanica icosahedral virus 2
Components
  • Virus: Haloarcula hispanica icosahedral virus 2
    • Protein or peptide: VP4
    • Protein or peptide: VP7
    • Protein or peptide: VP7
    • Protein or peptide: VP7
    • Protein or peptide: Uncharacterized protein
    • Protein or peptide: VP16 (vertex complex)
    • Protein or peptide: GPS III
    • Protein or peptide: polypeptide stretch (vertex complex)

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Supramolecule #1: Haloarcula hispanica icosahedral virus 2

SupramoleculeName: Haloarcula hispanica icosahedral virus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1154689 / Sci species name: Haloarcula hispanica icosahedral virus 2 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Haloarcula hispanica ATCC 33960 (Halophile)

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Macromolecule #1: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 1 / Details: http://mit.cicbiogune.int:39000/projects/P2/W1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica icosahedral virus 2
Molecular weightTheoretical: 25.585746 KDa
SequenceString: QTQEYTINHT GGVLGDSYVT TASNQTSPQR ETAVLSFECP RKFEEINYVG QRDATRFVPR TTESITGSAN DDTVVDLTAN IQPVAGEEV IAEQDYPVAV AYNVTQGVEV DVVDADYAAD TVTLGTNPAD GDEVKVWPIM SDGDVQFRLI NQFGQEEGRV Y PWSTPLYR ...String:
QTQEYTINHT GGVLGDSYVT TASNQTSPQR ETAVLSFECP RKFEEINYVG QRDATRFVPR TTESITGSAN DDTVVDLTAN IQPVAGEEV IAEQDYPVAV AYNVTQGVEV DVVDADYAAD TVTLGTNPAD GDEVKVWPIM SDGDVQFRLI NQFGQEEGRV Y PWSTPLYR WHDFPQLKRG REINLHGSAS WSENETLEIL LDAPQALTWE DSDYPRGQYV TTLEQDVEIT L

UniProtKB: VP4

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Macromolecule #2: VP7

MacromoleculeName: VP7 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica icosahedral virus 2
Molecular weightTheoretical: 18.473355 KDa
SequenceString:
PEIGNNGAEK QISLHKGQPF IDTQDVGAAD PNTPAVTIEG PSDYVIAIDA GTPVAPEFRD ANGDKLDPST RVTIQKCDKQ GNPLGDGIV FSDTLGRFEY SKMRSDPDYM RKTTTSLMID EREIVKIFVE VPPNANGMDA DNSRITIGDD TSDYGKAVGI V EHGDLSPA ESKA

UniProtKB: VP7

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Macromolecule #3: VP7

MacromoleculeName: VP7 / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica icosahedral virus 2
Molecular weightTheoretical: 18.857811 KDa
SequenceString:
PEIGNNGAEK QISLHKGQPF IDTQDVGAAD PNTPAVTIEG PSDYVIAIDA GTPVAPEFRD ANGDKLDPST RVTIQKCDKQ GNPLGDGIV FSDTLGRFEY SKMRSDPDYM RKTTTSLMID EREIVKIFVE VPPNANGMDA DNSRITIGDD TSDYGKAVGI V EHGDLSPA ESKAVRQ

UniProtKB: VP7

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Macromolecule #4: VP7

MacromoleculeName: VP7 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica icosahedral virus 2
Molecular weightTheoretical: 17.347154 KDa
SequenceString:
IGNNGAEKQI SLHKGQPFID TQDVGAADPN TPAVTIEGPS DYVIAIDAGT PVAPEFRDAN GDKLDPSTRV TIQKCDKQGN PLGDGIVFS DTLGRFEYSK MRSDPDYMRK TTTSLMIDER EIVKIFVEVP PNANGMDADN SRITIGDDTS DYGKAVGIVE H G

UniProtKB: VP7

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Macromolecule #5: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica icosahedral virus 2
Molecular weightTheoretical: 14.206529 KDa
SequenceString:
QTADGRVGLV PVNSYVTLET DDLDTDEHPV TDAGTVALEP GESAPIVRYD LGQPAAVYAV GATDEANVEY ELKVNNSKTV GGRTNSPLG VLNTPFSFVE KLGGAIPCET AATYWAHYSS DATGTVELAG RMHIEV

UniProtKB: Uncharacterized protein

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Macromolecule #6: VP16 (vertex complex)

MacromoleculeName: VP16 (vertex complex) / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica icosahedral virus 2
Molecular weightTheoretical: 18.485723 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)(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)(UNK)

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Macromolecule #7: GPS III

MacromoleculeName: GPS III / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica icosahedral virus 2
Molecular weightTheoretical: 8.954028 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)

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Macromolecule #8: polypeptide stretch (vertex complex)

MacromoleculeName: polypeptide stretch (vertex complex) / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica icosahedral virus 2
Molecular weightTheoretical: 2.145636 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)

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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
20.0 mMC4H11NO3Tris-HCL
20.0 mMMgCl2Magnessium clorhide
10.0 mMCaCl2Calcium clorhide
0.5 MNaClsodium clorhide
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 14877
Startup modelType of model: EMDB MAP
EMDB ID:

3109

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 11446
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)
Final 3D classificationSoftware - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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