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Yorodumi- EMDB-4015: A 3.9 Angstrom structure of HIV-1 CA-SP1 assembled in presence of... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4015 | |||||||||
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Title | A 3.9 Angstrom structure of HIV-1 CA-SP1 assembled in presence of Bevirimat | |||||||||
Map data | ||||||||||
Sample |
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Keywords | HIV-1 capsid SP1 / viral protein | |||||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding ...viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus type 1 group M subtype B (isolate NY5) / Human immunodeficiency virus 1 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Schur FKM / Obr M | |||||||||
Funding support | Germany, 2 items
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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_4015.map.gz | 25.2 MB | EMDB map data format | |
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Header (meta data) | emd-4015-v30.xml emd-4015.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_4015.png | 678.2 KB | ||
Filedesc metadata | emd-4015.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4015 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4015 | HTTPS FTP |
-Validation report
Summary document | emd_4015_validation.pdf.gz | 334.2 KB | Display | EMDB validaton report |
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Full document | emd_4015_full_validation.pdf.gz | 333.3 KB | Display | |
Data in XML | emd_4015_validation.xml.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4015 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4015 | HTTPS FTP |
-Related structure data
Related structure data | 5l93MC 4016C 4017C 4018C 4019C 4020C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10164 (Title: Cryo-electron tomography of immature HIV-1 dMACANC VLPs Data size: 865.0 Data #1: Compressed, unaligned, multi-frame micrographs of tilt series containing HIV-1 dMACANC virus like particles assembled in the presence of BVM. [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4015.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 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: all Details: Virus-like particles were obtained by in vitro assembly of a truncated Gag construct (deltaMACANCSP2) in presence of the maturation inhibitor Bevirimat 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) |
-Macromolecule #1: Capsid protein p24
Macromolecule | Name: Capsid protein p24 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus type 1 group M subtype B (isolate NY5) Strain: isolate NY5 |
Molecular weight | Theoretical: 24.789396 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SPRTLNAWVK VVEEKAFSPE VIPMFSALSE GATPQDLNTM LNTVGGHQAA MQMLKETINE EAAEWDRLHP VHAGPIAPGQ MREPRGSDI AGTTSTLQEQ IGWMTHNPPI PVGEIYKRWI ILGLNKIVRM YSPTSILDIR QGPKEPFRDY VDRFYKTLRA E QASQEVKN ...String: SPRTLNAWVK VVEEKAFSPE VIPMFSALSE GATPQDLNTM LNTVGGHQAA MQMLKETINE EAAEWDRLHP VHAGPIAPGQ MREPRGSDI AGTTSTLQEQ IGWMTHNPPI PVGEIYKRWI ILGLNKIVRM YSPTSILDIR QGPKEPFRDY VDRFYKTLRA E QASQEVKN WMTETLLVQN ANPDCKTILK ALGPGATLEE MMTACQGVGG PGHKARVLAE AMSQVT UniProtKB: Gag polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
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 / Pretreatment - Time: 30 sec. / 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 |
-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: 8-10 / Number grids imaged: 2 / Average exposure time: 1.0 sec. / Average electron dose: 3.4 e/Å2 Details: Number of frames ranged from 8-10 Exposure time per tilt ranged from 0.8 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: 5.0 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 | Number classes used: 1 / Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: AV3, TOM Toolbox) / Number subtomograms used: 128733 |
Extraction | Number tomograms: 43 / Number images used: 527528 Details: Subtomograms were extracted from the surface of each particle according to the determined radius of the particle. |
Final angle assignment | Type: OTHER / Software: (Name: AV3, TOM Toolbox) / Details: Cross-correlation based template matching |
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: OTHER | ||||||||
Output model | PDB-5l93: |