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Yorodumi- EMDB-3473: The structure of the mature HIV-1 CA hexameric lattice with curva... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3473 | |||||||||
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Title | The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=11, twist=0 | |||||||||
Map data | The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=11, twist=0 | |||||||||
Sample |
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Keywords | retrovirus / HIV-1 / capsid / lattice curvature / viral protein | |||||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / viral process / viral capsid / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / structural molecule activity / virion membrane / RNA binding ...viral budding via host ESCRT complex / viral process / viral capsid / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 8.2 Å | |||||||||
Authors | Mattei S / Glass B | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Science / Year: 2016 Title: The structure and flexibility of conical HIV-1 capsids determined within intact virions. Authors: Simone Mattei / Bärbel Glass / Wim J H Hagen / Hans-Georg Kräusslich / John A G Briggs / Abstract: HIV-1 contains a cone-shaped capsid encasing the viral genome. This capsid is thought to follow fullerene geometry-a curved hexameric lattice of the capsid protein, CA, closed by incorporating 12 CA ...HIV-1 contains a cone-shaped capsid encasing the viral genome. This capsid is thought to follow fullerene geometry-a curved hexameric lattice of the capsid protein, CA, closed by incorporating 12 CA pentamers. Current models for core structure are based on crystallography of hexameric and cross-linked pentameric CA, electron microscopy of tubular CA arrays, and simulations. Here, we report subnanometer-resolution cryo-electron tomography structures of hexameric and pentameric CA within intact HIV-1 particles. Whereas the hexamer structure is compatible with crystallography studies, the pentamer forms using different interfaces. Determining multiple structures revealed how CA flexes to form the variably curved core shell. We show that HIV-1 CA assembles both aberrant and perfect fullerene cones, supporting models in which conical cores assemble de novo after maturation. | |||||||||
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_3473.map.gz | 14.6 MB | EMDB map data format | |
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Header (meta data) | emd-3473-v30.xml emd-3473.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_3473.png | 255.5 KB | ||
Filedesc metadata | emd-3473.cif.gz | 6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3473 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3473 | HTTPS FTP |
-Validation report
Summary document | emd_3473_validation.pdf.gz | 258.8 KB | Display | EMDB validaton report |
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Full document | emd_3473_full_validation.pdf.gz | 257.9 KB | Display | |
Data in XML | emd_3473_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3473 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3473 | HTTPS FTP |
-Related structure data
Related structure data | 5md5MC 3464C 3465C 3466C 3467C 3468C 3469C 3470C 3471C 3472C 3474C 3475C 3477C 3478C 3479C 3480C 3481C 3482C 3483C 3484C 3485C 5mcxC 5mcyC 5mczC 5md0C 5md1C 5md2C 5md3C 5md4C 5md6C 5md7C 5md8C 5md9C 5mdaC 5mdbC 5mdcC 5mddC 5mdeC 5mdfC 5mdgC M: atomic model generated by this map C: citing same article (ref.) |
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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_3473.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=11, twist=0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.78 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: HIV-1 particles were produced by infection of MT-4 cells with HIV-1 strain NL43 by coculture. NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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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: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: NL43 |
Molecular weight | Theoretical: 8.370568 KDa |
Sequence | String: TSILDIRQGP KEPFRDYVDR FYKTLRAEQA SQEVKNWMTE TLLVQNANPD CKTILKALGP GATLEEMMTA CQGV UniProtKB: Gag protein |
-Macromolecule #2: Capsid protein p24
Macromolecule | Name: Capsid protein p24 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: NL43 |
Molecular weight | Theoretical: 16.301689 KDa |
Sequence | String: PIVQNLQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSP UniProtKB: Gag protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Component - Name: PBS |
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Grid | Model: C-flat / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 292 K / Instrument: FEI VITROBOT MARK II Details: 10nm colloidal gold was added to the sample prior to plunge freezing. |
Details | Viral particles were purified from cell culture supernatant by iodixanol gradient centrifugation. |
-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 / Number grids imaged: 1 / Average electron dose: 2.2 e/Å2 |
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: 6.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 81000 |
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: AV3, TOM Toolbox) Details: The final reconstruction is obtained by averaging, without further alignment, subtomograms that were selected based on the local curvature of the hexameric lattice. This reconstruction has ...Details: The final reconstruction is obtained by averaging, without further alignment, subtomograms that were selected based on the local curvature of the hexameric lattice. This reconstruction has hexamer-hexamer curvature parameters: tilt=11, twist=0. Number subtomograms used: 17239 |
Extraction | Number tomograms: 103 / Number images used: 652618 / Reference model: reference free Details: Subtomograms were extracted along the manually rendered core surface of each viral particle. |
Final angle assignment | Type: OTHER / Software: (Name: AV3, TOM Toolbox) / Details: Cross-correlation based template matching. |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient |
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Output model | PDB-5md5: |