|Entry||Database: PDB / ID: 5md4|
|Title||The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=11, twist=6|
|Descriptor||Capsid protein p24|
|Keywords||VIRAL PROTEIN / retrovirus / HIV-1 / capsid / lattice curvature / Viral protein|
|Specimen source||Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1|
|Method||Electron microscopy (8.4 Å resolution / Particle / Subtomogram averaging)|
|Authors||Mattei, S. / Glass, B. / Hagen, W.J.H. / Kraeusslich, H.-G. / Briggs, J.A.G.|
|Citation||Science, 2016, 354, 1434-1437|
SummaryFull reportAbout validation report
|Date||Deposition: Nov 10, 2016 / Release: Dec 28, 2016|
Downloads & links
A: Capsid protein p24
B: Capsid protein p24
F: Capsid protein p24
W: Capsid protein p24
a: Capsid protein p24
b: Capsid protein p24
f: Capsid protein p24
C: Capsid protein p24
D: Capsid protein p24
E: Capsid protein p24
G: Capsid protein p24
H: Capsid protein p24
I: Capsid protein p24
J: Capsid protein p24
Mass: 8370.568 Da / Num. of mol.: 8 / Fragment: C-terminal domain, UNP residues 141-214
Source: (natural) Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
References: UniProt: A0A0K0V8J8
Mass: 16301.689 Da / Num. of mol.: 6 / Fragment: N-terminal domain, UNP residues 123-269
Source: (natural) Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
References: UniProt: E9MJT0
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SUBTOMOGRAM AVERAGING|
|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: 1, 2 / Source: NATURAL
|Source (natural)||Organism: Human immunodeficiency virus 1|
|Details of virus||Empty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION|
|Natural host||Organism: Homo sapiens|
|Buffer solution||pH: 7.4|
|Buffer component||Name: PBS|
|Specimen||Details: Viral particles were purified from cell culture supernatant by iodixanol gradient centrifugation.|
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
|Specimen support||Grid material: COPPER / Grid mesh size: 300 / Grid type: C-flat|
|Vitrification||Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 292 kelvins|
Details: 10nm colloidal gold was added to the sample prior to plunge freezing
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS / Details: Nanoprobe|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 81000 / Nominal defocus max: 6500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 mm / 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) / Number of grids imaged: 1|
|EM imaging optics||Energyfilter name: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV|
|Image scans||Dimension width: 3710 / Dimension height: 3838 / Movie frames/image: 5|
|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|
|3D reconstruction||Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number 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 hexamer-hexamer curvature parameters: tilt=11, twist=6.
Number of class averages: 1 / Symmetry type: POINT
|EM volume selection||Details: Subtomograms were extracted along the manually rendered core surface of each viral particle.|
Number of tomograms: 103 / Number of volumes extracted: 652618 / Reference model: reference free
|Atomic model building||Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Cross-correlation coefficient|
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