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- EMDB-13079: Representative cryo-electron tomogram of HIV-1 MA-SP1 particles -

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Basic information

Entry
Database: EMDB / ID: EMD-13079
TitleRepresentative cryo-electron tomogram of HIV-1 MA-SP1 particles
Map dataRepresentative cryo-electron tomogram of HIV-1 MA-SP1 particles
Sample
  • Virus: Human immunodeficiency virus 1
Biological speciesHuman immunodeficiency virus 1
Methodelectron tomography / cryo EM
AuthorsMattei S / Tan AWK / Glass B / Mueller B / Kraeusslich HG / Briggs JAG
Funding support Germany, United Kingdom, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)BR 3635/2-1 Germany
German Research Foundation (DFG)KR 906/7-1 Germany
German Research Foundation (DFG)KR 906/8-1 Germany
German Research Foundation (DFG)MU 885/5-1 Germany
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: High-resolution structures of HIV-1 Gag cleavage mutants determine structural switch for virus maturation.
Authors: Simone Mattei / Aaron Tan / Bärbel Glass / Barbara Müller / Hans-Georg Kräusslich / John A G Briggs /
Abstract: HIV-1 maturation occurs via multiple proteolytic cleavages of the Gag polyprotein, causing rearrangement of the virus particle required for infectivity. Cleavage results in beta-hairpin formation at ...HIV-1 maturation occurs via multiple proteolytic cleavages of the Gag polyprotein, causing rearrangement of the virus particle required for infectivity. Cleavage results in beta-hairpin formation at the N terminus of the CA (capsid) protein and loss of a six-helix bundle formed by the C terminus of CA and the neighboring SP1 peptide. How individual cleavages contribute to changes in protein structure and interactions, and how the mature, conical capsid forms, are poorly understood. Here, we employed cryoelectron tomography to determine morphology and high-resolution CA lattice structures for HIV-1 derivatives in which Gag cleavage sites are mutated. These analyses prompt us to revise current models for the crucial maturation switch. Unlike previously proposed, cleavage on either terminus of CA was sufficient, in principle, for lattice maturation, while complete processing was needed for conical capsid formation. We conclude that destabilization of the six-helix bundle, rather than beta-hairpin formation, represents the main determinant of structural maturation.
History
DepositionJun 14, 2021-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateJun 23, 2021-
Current statusJun 23, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Movie viewer
Supplemental images

emd_13079.png

Downloads & links

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Map

FileDownload / File: emd_13079.map.gz / Format: CCP4 / Size: 81.8 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationRepresentative cryo-electron tomogram of HIV-1 MA-SP1 particles
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.8 Å/pix.
x 200 pix.
= 2160. Å		10.8 Å/pix.
x 463 pix.
= 5000.4 Å		10.8 Å/pix.
x 463 pix.
= 5000.4 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.8 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-262.0 - 306.0
Average (Standard dev.)8.869334 (±41.008083)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions463463200
Spacing463463200
CellA: 5000.4 Å / B: 5000.4 Å / C: 2160.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z10.810.810.8
M x/y/z463463200
origin x/y/z0.0000.0000.000
length x/y/z5000.4005000.4002160.000
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS463463200
D min/max/mean-262.000306.0008.869

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Supplemental data

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Sample components

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Entire : Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Components
  • Virus: Human immunodeficiency virus 1

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Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0
Details: cHIV MA-SP1 Gag proteolytic cleavage mutant virus particles purified from HEK293T cells.
NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host systemOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE
DetailscHIV MA-SP1 Gag proteolytic cleavage mutant virus particles purified from HEK293T cells.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: homemade / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 1
CTF correctionSoftware: (Name: CTFFIND, IMOD)

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