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Yorodumi- EMDB-4019: Cryo-electron tomogram containing HIV-1 deltaMACANC virus-like pa... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4019 | |||||||||
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Title | Cryo-electron tomogram containing HIV-1 deltaMACANC virus-like particles assembled in vitro | |||||||||
Map data | None | |||||||||
Sample |
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Biological species | Human immunodeficiency virus 1 | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Schur FKM / Obr M / Hagen WJH / Wan W / Arjen JJ / Kirkpatrick JM / Sachse C / Kraeusslich H-G / Briggs JAG | |||||||||
Citation | Journal: Science / Year: 2016 Title: An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. Authors: Florian K M Schur / Martin Obr / Wim J H Hagen / William Wan / Arjen J Jakobi / Joanna M Kirkpatrick / Carsten Sachse / Hans-Georg Kräusslich / John A G Briggs / Abstract: Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation ...Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity. The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator of assembly and maturation and is the target of MIs. We applied optimized cryo-electron tomography and subtomogram averaging to resolve this region within assembled immature HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure reveals a network of intra- and intermolecular interactions mediating immature HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible to protease. We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure, and MI resistance develops by destabilizing CA-SP1. | |||||||||
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_4019.map.gz | 15.6 MB | EMDB map data format | |
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Header (meta data) | emd-4019-v30.xml emd-4019.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
Images | emd_4019.png | 882.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4019 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4019 | HTTPS FTP |
-Validation report
Summary document | emd_4019_validation.pdf.gz | 181.4 KB | Display | EMDB validaton report |
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Full document | emd_4019_full_validation.pdf.gz | 180.5 KB | Display | |
Data in XML | emd_4019_validation.xml.gz | 3.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4019 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4019 | HTTPS FTP |
-Related 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_4019.map.gz / Format: CCP4 / Size: 61.3 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 10.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human immunodeficiency virus 1
Entire | Name: Human immunodeficiency virus 1 |
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Components |
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-Supramolecule #1: Human immunodeficiency virus 1
Supramolecule | Name: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Virus-like particles were obtained by in vitro assembly of a truncated Gag construct (deltaMACANCSP2) NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) |
Host system | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET11C |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
Details: Virus-like particles were assembled in the presence of nucleic acid (73mer oligonucleotide, 1:10 molar ratio oligonucleotide:protein). | |||||||||||||||
Grid | Model: C-flat / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: at 20 mA | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 15 K / Instrument: FEI VITROBOT MARK II Details: 10nM colloidal gold was added to the sample prior to plunge freezing.. | |||||||||||||||
Details | Virus-like particles were assembled in vitro | |||||||||||||||
Sectioning | Other: NO SECTIONING | |||||||||||||||
Fiducial marker | Manufacturer: CMC Utrecht / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Details | Nanoprobe |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 6-10 / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 5.0 e/Å2 Details: Number of frames ranged from 6-10 Exposure time per tilt ranged from 0.6 to 1.0 seconds |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
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
Details | Frames were aligned using MotionCorr. Tilts in a tilt series were exposure filtered for cumulative electron dose. Tomograms were reconstructed using IMOD. | ||||||
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Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD / Details: Tomograms were reconstructed in IMOD / Number images used: 41 | ||||||
CTF correction | Software:
Details: CTF correction was performed using the ctfphaseflip program in IMOD prior to backprojection. |