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Yorodumi- EMDB-0174: Cryo-EM structure of archaeal extremophilic internal membrane-con... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0174 | |||||||||||||||
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Title | Cryo-EM structure of archaeal extremophilic internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) at 3.74 Angstroms resolution. | |||||||||||||||
Map data | Centered map 0 0 0 | |||||||||||||||
Sample |
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Function / homology | VP7 / VP4 / VP9 Function and homology information | |||||||||||||||
Biological species | Haloarcula californiae ATCC 33799 (Halophile) / Haloarcula californiae icosahedral virus 1 | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.74 Å | |||||||||||||||
Authors | Abrescia NG / Santos-Perez I / Charro D | |||||||||||||||
Funding support | Spain, Finland, 4 items
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Citation | Journal: 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 |
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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_0174.map.gz | 1.6 GB | EMDB map data format | |
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Header (meta data) | emd-0174-v30.xml emd-0174.xml | 29 KB 29 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0174_fsc.xml | 27 KB | Display | FSC data file |
Images | emd_0174.png | 197.5 KB | ||
Masks | emd_0174_msk_1.map | 1.7 GB | Mask map | |
Others | emd_0174_additional.map.gz emd_0174_half_map_1.map.gz emd_0174_half_map_2.map.gz | 1.6 GB 1.4 GB 1.4 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0174 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0174 | HTTPS FTP |
-Related structure data
Related structure data | 6h9cMC 0050C 0072C 0073C 0131C 0172C 6h82C 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_0174.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Centered map 0 0 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 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_0174_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_0174_additional.map | ||||||||||||
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Density Histograms |
-Half map: None
File | emd_0174_half_map_1.map | ||||||||||||
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Annotation | None | ||||||||||||
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Density Histograms |
-Half map: None
File | emd_0174_half_map_2.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Haloarcula californiae icosahedral virus 1
Entire | Name: Haloarcula californiae icosahedral virus 1 |
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Components |
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-Supramolecule #1: Haloarcula californiae icosahedral virus 1
Supramolecule | Name: 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 |
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Host (natural) | Organism: Haloarcula californiae ATCC 33799 (Halophile) |
Virus shell | Shell ID: 1 / Diameter: 800.0 Å / T number (triangulation number): 28 |
-Macromolecule #1: VP7
Macromolecule | Name: VP7 / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO |
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Source (natural) | Organism: Haloarcula californiae ATCC 33799 (Halophile) |
Molecular weight | Theoretical: 19.912832 KDa |
Sequence | String: MGNIGNLSAE KQISLYDGQP FISEQDVAAG DPNTPALTIE GPDGYVIAVD AGTPIAPEFR DSNGEKLDPS TRVIVQKCDR QGNPLGDGI IFNDTLGRFN YNKMRTDPDY MRKTAKSLMV DEREIVKVFV DVPDGANGYD AERSRFTLGD DTSDFGKAVE I VDHDDLTE GETQAVKSAS QRSGGA |
-Macromolecule #2: VP9
Macromolecule | Name: VP9 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Haloarcula californiae ATCC 33799 (Halophile) |
Molecular weight | Theoretical: 16.271062 KDa |
Sequence | String: MRDNQDLLVK RLGRLVNVLE SKEFGGTTTV DKDLDVTKNV TRTDEPNEDN TPDYFSTGKD RVLVPDTEEW ERLGFGIVAK TVNVRTTDD VLLAFANPNT NGPTFKIRSN ESPFTIGGDA GIDTAFMWLK KAESAQNDPA VEIIAYR |
-Macromolecule #3: GPS-III molecule located underneath the capsomer close to the ico...
Macromolecule | Name: 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 |
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Source (natural) | Organism: Haloarcula californiae ATCC 33799 (Halophile) |
Molecular weight | Theoretical: 9.209344 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) |
-Macromolecule #4: GPS-II protein located underneath the two-tower capsomer NOT sitt...
Macromolecule | Name: 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 |
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Source (natural) | Organism: Haloarcula californiae ATCC 33799 (Halophile) |
Molecular weight | Theoretical: 6.400881 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) |
-Macromolecule #5: (Half) GPS-II protein located underneath the two-tower capsomer s...
Macromolecule | Name: (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 |
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Source (natural) | Organism: Haloarcula californiae ATCC 33799 (Halophile) |
Molecular weight | Theoretical: 3.932839 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) |
-Macromolecule #6: Peripentonal unknown polypeptide
Macromolecule | Name: Peripentonal unknown polypeptide / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Haloarcula californiae ATCC 33799 (Halophile) |
Molecular weight | Theoretical: 1.549902 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) |
-Macromolecule #7: VP4
Macromolecule | Name: VP4 / type: protein_or_peptide / ID: 7 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Haloarcula californiae ATCC 33799 (Halophile) |
Molecular weight | Theoretical: 25.995318 KDa |
Sequence | String: 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 |
-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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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III | ||||||||||||||||||
Details | Haloarcula californiae icosahedral virus 1. Taxonomic identifier 1735722 NCBI. |
-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 / Cs: 2.7 mm / Nominal defocus max: 3.9 µm / Nominal defocus min: 0.6 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film 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 |
-Image processing
-Atomic model buiding 1
Details | The 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). |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 89.1 / Target criteria: Cross-correlation coefficient |
Output model | PDB-6h9c: |