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Yorodumi- EMDB-0172: Cryo-EM structure of the archaeal extremophilic internal membrane... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0172 | |||||||||||||||
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Title | Cryo-EM structure of the archaeal extremophilic internal membrane containing Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.78 Angstroms resolution. | |||||||||||||||
Map data | Map derived from RELION postprocessed map. The map was then centred at 0,0,0 and finally used for model refinement. | |||||||||||||||
Sample |
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Keywords | single vertical beta-barrel virus / archaeal / membrane-containing / quasi-atomic resolution / VIRUS | |||||||||||||||
Function / homology | VP7 / VP4 / Uncharacterized protein Function and homology information | |||||||||||||||
Biological species | Haloarcula hispanica icosahedral virus 2 | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.78 Å | |||||||||||||||
Authors | Abrescia NG / Santos-Perez I | |||||||||||||||
Funding support | Spain, Finland, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0172.map.gz | 1.5 GB | EMDB map data format | |
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Header (meta data) | emd-0172-v30.xml emd-0172.xml | 29.9 KB 29.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0172_fsc.xml | 26.8 KB | Display | FSC data file |
Images | emd_0172.png | 219.2 KB | ||
Masks | emd_0172_msk_1.map | 1.6 GB | Mask map | |
Filedesc metadata | emd-0172.cif.gz | 6.8 KB | ||
Others | emd_0172_additional.map.gz emd_0172_half_map_1.map.gz emd_0172_half_map_2.map.gz | 1.5 GB 1.3 GB 1.3 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0172 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0172 | HTTPS FTP |
-Related structure data
Related structure data | 6h82MC 0050C 0072C 0073C 0131C 0174C 6h9cC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0172.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map derived from RELION postprocessed map. The map was then centred at 0,0,0 and finally used for model refinement. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_0172_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Relion post-processed map bfactor -40
File | emd_0172_additional.map | ||||||||||||
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Annotation | Relion post-processed map bfactor -40 | ||||||||||||
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Density Histograms |
-Half map: Half maps for gold-standard FSC and generation of...
File | emd_0172_half_map_1.map | ||||||||||||
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Annotation | Half maps for gold-standard FSC and generation of both submitted postprocessed maps. | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_0172_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Haloarcula hispanica icosahedral virus 2
Entire | Name: Haloarcula hispanica icosahedral virus 2 |
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Components |
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-Supramolecule #1: Haloarcula hispanica icosahedral virus 2
Supramolecule | Name: 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 |
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Host (natural) | Organism: Haloarcula hispanica ATCC 33960 (Halophile) |
-Macromolecule #1: VP4
Macromolecule | Name: VP4 / type: protein_or_peptide / ID: 1 / Details: http://mit.cicbiogune.int:39000/projects/P2/W1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Haloarcula hispanica icosahedral virus 2 |
Molecular weight | Theoretical: 25.585746 KDa |
Sequence | String: 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 |
-Macromolecule #2: VP7
Macromolecule | Name: VP7 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Haloarcula hispanica icosahedral virus 2 |
Molecular weight | Theoretical: 18.473355 KDa |
Sequence | String: PEIGNNGAEK QISLHKGQPF IDTQDVGAAD PNTPAVTIEG PSDYVIAIDA GTPVAPEFRD ANGDKLDPST RVTIQKCDKQ GNPLGDGIV FSDTLGRFEY SKMRSDPDYM RKTTTSLMID EREIVKIFVE VPPNANGMDA DNSRITIGDD TSDYGKAVGI V EHGDLSPA ESKA UniProtKB: VP7 |
-Macromolecule #3: VP7
Macromolecule | Name: VP7 / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Haloarcula hispanica icosahedral virus 2 |
Molecular weight | Theoretical: 18.857811 KDa |
Sequence | String: PEIGNNGAEK QISLHKGQPF IDTQDVGAAD PNTPAVTIEG PSDYVIAIDA GTPVAPEFRD ANGDKLDPST RVTIQKCDKQ GNPLGDGIV FSDTLGRFEY SKMRSDPDYM RKTTTSLMID EREIVKIFVE VPPNANGMDA DNSRITIGDD TSDYGKAVGI V EHGDLSPA ESKAVRQ UniProtKB: VP7 |
-Macromolecule #4: VP7
Macromolecule | Name: VP7 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Haloarcula hispanica icosahedral virus 2 |
Molecular weight | Theoretical: 17.347154 KDa |
Sequence | String: IGNNGAEKQI SLHKGQPFID TQDVGAADPN TPAVTIEGPS DYVIAIDAGT PVAPEFRDAN GDKLDPSTRV TIQKCDKQGN PLGDGIVFS DTLGRFEYSK MRSDPDYMRK TTTSLMIDER EIVKIFVEVP PNANGMDADN SRITIGDDTS DYGKAVGIVE H G UniProtKB: VP7 |
-Macromolecule #5: Uncharacterized protein
Macromolecule | Name: Uncharacterized protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Haloarcula hispanica icosahedral virus 2 |
Molecular weight | Theoretical: 14.206529 KDa |
Sequence | String: QTADGRVGLV PVNSYVTLET DDLDTDEHPV TDAGTVALEP GESAPIVRYD LGQPAAVYAV GATDEANVEY ELKVNNSKTV GGRTNSPLG VLNTPFSFVE KLGGAIPCET AATYWAHYSS DATGTVELAG RMHIEV UniProtKB: Uncharacterized protein |
-Macromolecule #6: VP16 (vertex complex)
Macromolecule | Name: VP16 (vertex complex) / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Haloarcula hispanica icosahedral virus 2 |
Molecular weight | Theoretical: 18.485723 KDa |
Sequence | 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) ...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) |
-Macromolecule #7: GPS III
Macromolecule | Name: GPS III / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Haloarcula hispanica icosahedral virus 2 |
Molecular weight | Theoretical: 8.954028 KDa |
Sequence | 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) ...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) |
-Macromolecule #8: polypeptide stretch (vertex complex)
Macromolecule | Name: polypeptide stretch (vertex complex) / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Haloarcula hispanica icosahedral virus 2 |
Molecular weight | Theoretical: 2.145636 KDa |
Sequence | 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) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.2 mg/mL | |||||||||||||||
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Buffer | pH: 7.2 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 | |||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 35.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |