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Yorodumi- EMDB-2708: The structure of the immature HIV-1 capsid in intact virus partic... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2708 | |||||||||
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Title | The structure of the immature HIV-1 capsid in intact virus particles at sub-nm resolution | |||||||||
Map data | Cryo-electron tomogram of immature HIV-1 particles treated with the protease inhibitor Amprenavir | |||||||||
Sample |
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Keywords | immature HIV / Retrovirus / Maturation / capsid / Gag | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Schur FKM / Hagen WJH / Rumlova M / Ruml T / Mueller B / Kraeusslich H-G / Briggs JAG | |||||||||
Citation | Journal: Nature / Year: 2015 Title: Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Authors: Florian K M Schur / Wim J H Hagen / Michaela Rumlová / Tomáš Ruml / Barbara Müller / Hans-Georg Kräusslich / John A G Briggs / Abstract: Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages. First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein lattice at the plasma membrane of the ...Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages. First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein lattice at the plasma membrane of the infected cell, inducing budding and release of an immature particle. Second, Gag is cleaved by the viral protease, leading to internal rearrangement of the virus into the mature, infectious form. Immature and mature HIV-1 particles are heterogeneous in size and morphology, preventing high-resolution analysis of their protein arrangement in situ by conventional structural biology methods. Here we apply cryo-electron tomography and sub-tomogram averaging methods to resolve the structure of the capsid lattice within intact immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning of all α-helices. The resulting model reveals tertiary and quaternary structural interactions that mediate HIV-1 assembly. Strikingly, these interactions differ from those predicted by the current model based on in vitro-assembled arrays of Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference, we solve the structure of the capsid lattice within intact immature Mason-Pfizer monkey virus particles. Comparison with the immature HIV-1 structure reveals that retroviral capsid proteins, while having conserved tertiary structures, adopt different quaternary arrangements during virus assembly. The approach demonstrated here should be applicable to determine structures of other proteins at subnanometre resolution within heterogeneous environments. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2708.map.gz | 6.3 GB | EMDB map data format | |
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Header (meta data) | emd-2708-v30.xml emd-2708.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_2708.tif | 762.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2708 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2708 | HTTPS FTP |
-Validation report
Summary document | emd_2708_validation.pdf.gz | 143.4 KB | Display | EMDB validaton report |
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Full document | emd_2708_full_validation.pdf.gz | 142.5 KB | Display | |
Data in XML | emd_2708_validation.xml.gz | 3.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2708 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2708 | 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_2708.map.gz / Format: CCP4 / Size: 6.7 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-electron tomogram of immature HIV-1 particles treated with the protease inhibitor Amprenavir | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.025 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 : immature HIV-1 particles treated with the protease inhibitor Ampr...
Entire | Name: immature HIV-1 particles treated with the protease inhibitor Amprenavir |
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Components |
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-Supramolecule #1000: immature HIV-1 particles treated with the protease inhibitor Ampr...
Supramolecule | Name: immature HIV-1 particles treated with the protease inhibitor Amprenavir type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Human immunodeficiency virus 1
Supramolecule | Name: Human immunodeficiency virus 1 / type: virus / ID: 1 / Name.synonym: HIV-1 / NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No / Syn species name: HIV-1 |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 / Details: 25mM MES pH 6.5, 150mM NaCl |
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Grid | Details: C-Flat 2/2-2C glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II Method: Degassed C-Flat 2/2-2C grids were glow discharged for 30 seconds at 20 mA. Virus solution was diluted in PBS containing 10nm colloidal gold. 2 ul of this mixture was applied to a grid. Blotting time: 2 seconds |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at nominal working magnification |
Specialist optics | Energy filter - Name: GATAN GIF 2002 |
Date | Aug 13, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN MULTISCAN / Average electron dose: 40 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -45 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 3 ° |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | CTF correction was performed on each projection |
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Final reconstruction | Software - Name: IMOD / Number images used: 36 |
CTF correction | Details: CTF correction was performed on each projection |