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- PDB-5md4: The structure of the mature HIV-1 CA hexameric lattice with curva... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5md4 | |||||||||
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Title | The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=11, twist=6 | |||||||||
![]() | (Capsid protein p24) x 2 | |||||||||
![]() | VIRAL PROTEIN / retrovirus / HIV-1 / capsid / lattice curvature | |||||||||
Function / homology | ![]() viral budding via host ESCRT complex / viral process / viral capsid / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 8.4 Å | |||||||||
![]() | Mattei, S. / Glass, B. / Hagen, W.J.H. / Kraeusslich, H.-G. / Briggs, J.A.G. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.9 KB | Display | ![]() |
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PDB format | ![]() | 109.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3472MC ![]() 3464C ![]() 3465C ![]() 3466C ![]() 3467C ![]() 3468C ![]() 3469C ![]() 3470C ![]() 3471C ![]() 3473C ![]() 3474C ![]() 3475C ![]() 3477C ![]() 3478C ![]() 3479C ![]() 3480C ![]() 3481C ![]() 3482C ![]() 3483C ![]() 3484C ![]() 3485C ![]() 5mcxC ![]() 5mcyC ![]() 5mczC ![]() 5md0C ![]() 5md1C ![]() 5md2C ![]() 5md3C ![]() 5md5C ![]() 5md6C ![]() 5md7C ![]() 5md8C ![]() 5md9C ![]() 5mdaC ![]() 5mdbC ![]() 5mdcC ![]() 5mddC ![]() 5mdeC ![]() 5mdfC ![]() 5mdgC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 8370.568 Da / Num. of mol.: 8 / Fragment: C-terminal domain, UNP residues 141-214 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 16301.689 Da / Num. of mol.: 6 / Fragment: N-terminal domain, UNP residues 123-269 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
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Sample preparation
Component | Name: Human immunodeficiency virus 1 / Type: VIRUS Details: HIV-1 particles were produced by infection of MT-4 cells with HIV-1 strain NL43 by coculture. Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Homo sapiens |
Buffer solution | pH: 7.4 |
Buffer component | Name: PBS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Viral particles were purified from cell culture supernatant by iodixanol gradient centrifugation. |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 292 K Details: 10nm colloidal gold was added to the sample prior to plunge freezing |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Details: Nanoprobe |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 6500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 2.2 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV |
Image scans | Width: 3710 / Height: 3838 / Movie frames/image: 5 |
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Processing
EM software |
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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. | ||||||||||||||||||||||||
CTF correction | Details: CTF correction was performed using the ctfphaseflip program in IMOD prior to backprojection. Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15789 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=6. Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
EM volume selection | Details: Subtomograms were extracted along the manually rendered core surface of each viral particle. Num. of tomograms: 103 / Num. of volumes extracted: 652618 / Reference model: reference free | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient |