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Yorodumi- EMDB-10297: Human endogenous retrovirus (HML2) mature capsid assembly, D6 capsule -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10297 | ||||||||||||
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Title | Human endogenous retrovirus (HML2) mature capsid assembly, D6 capsule | ||||||||||||
Map data | Sharpened map | ||||||||||||
Sample |
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Function / homology | Function and homology information nucleic acid binding / viral translational frameshifting / structural molecule activity / zinc ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.77 Å | ||||||||||||
Authors | Acton OJH / Taylor IA / Rosenthal PB | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structural basis for Fullerene geometry in a human endogenous retrovirus capsid. Authors: Oliver Acton / Tim Grant / Giuseppe Nicastro / Neil J Ball / David C Goldstone / Laura E Robertson / Kasim Sader / Andrea Nans / Andres Ramos / Jonathan P Stoye / Ian A Taylor / Peter B Rosenthal / Abstract: The HML2 (HERV-K) group constitutes the most recently acquired family of human endogenous retroviruses, with many proviruses less than one million years old. Many maintain intact open reading frames ...The HML2 (HERV-K) group constitutes the most recently acquired family of human endogenous retroviruses, with many proviruses less than one million years old. Many maintain intact open reading frames and provirus expression together with HML2 particle formation are observed in early stage human embryo development and are associated with pluripotency as well as inflammatory disease, cancers and HIV-1 infection. Here, we reconstruct the core structural protein (CA) of an HML2 retrovirus, assemble particles in vitro and employ single particle cryogenic electron microscopy (cryo-EM) to determine structures of four classes of CA Fullerene shell assemblies. These icosahedral and capsular assemblies reveal at high-resolution the molecular interactions that allow CA to form both pentamers and hexamers and show how invariant pentamers and structurally plastic hexamers associate to form the unique polyhedral structures found in retroviral cores. | ||||||||||||
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_10297.map.gz | 676.9 MB | EMDB map data format | |
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Header (meta data) | emd-10297-v30.xml emd-10297.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_10297.png | 60.9 KB | ||
Others | emd_10297_additional.map.gz | 676.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10297 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10297 | HTTPS FTP |
-Validation report
Summary document | emd_10297_validation.pdf.gz | 340.7 KB | Display | EMDB validaton report |
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Full document | emd_10297_full_validation.pdf.gz | 339.8 KB | Display | |
Data in XML | emd_10297_validation.xml.gz | 8.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10297 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10297 | HTTPS FTP |
-Related structure data
Related structure data | 6sslMC 6sa9C 6saiC 6ssjC 6sskC 6ssmC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10297.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_10297_additional.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human endogenous retrovirus (HML2) mature capsid assembly, D6 capsule
Entire | Name: Human endogenous retrovirus (HML2) mature capsid assembly, D6 capsule |
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Components |
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-Supramolecule #1: Human endogenous retrovirus (HML2) mature capsid assembly, D6 capsule
Supramolecule | Name: Human endogenous retrovirus (HML2) mature capsid assembly, D6 capsule type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 3.1 MDa |
-Macromolecule #1: Endogenous retrovirus group K member 24 Gag polyprotein
Macromolecule | Name: Endogenous retrovirus group K member 24 Gag polyprotein type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 27.570488 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: PVTLEPMPPG EGAQEGEPPT VEARYKSFSI KMLKDMKEGV KQYGPNSPYM RTLLDSIAHG HRLIPYDWEI LAKSSLSPSQ FLQFKTWWI DGVQEQVRRN RAANPPVNID ADQLLGIGQN WSTISQQALM QNEAIEQVRA ICLRAWEKIQ DPGSACPSFN T VRQGSKEP ...String: PVTLEPMPPG EGAQEGEPPT VEARYKSFSI KMLKDMKEGV KQYGPNSPYM RTLLDSIAHG HRLIPYDWEI LAKSSLSPSQ FLQFKTWWI DGVQEQVRRN RAANPPVNID ADQLLGIGQN WSTISQQALM QNEAIEQVRA ICLRAWEKIQ DPGSACPSFN T VRQGSKEP YPDFVARLQD VAQKSIADEK ARKVIVELMA YENANPECQS AIKPLKGKVP AGSDVISEYV KACDGIGGAM HK AMLMAQL E |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 16 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 10935 / Average exposure time: 60.0 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 4.1) |
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Final reconstruction | Applied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 16723 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 90 / Target criteria: map vs model FSC |
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Output model | PDB-6ssl: |