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- EMDB-20574: TRIM5alpha-coated HIV-1 capsid tube -

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Basic information

Entry
Database: EMDB / ID: EMD-20574
TitleTRIM5alpha-coated HIV-1 capsid tube
Map dataRepresentative tomogram of a TRIM5alpha-coated HIV-1 CA tube
Sample
  • Virus: Human immunodeficiency virus 1
Biological speciesHuman immunodeficiency virus 1
Methodelectron tomography / cryo EM
AuthorsSkorupka KA / Pornillos O / Ganser-Pornillos BK
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesR01-GM112508 United States
National Institutes of Health/National Institute of General Medical SciencesP50-GM082545 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesR01-AI150479 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesP50-AI150464 United States
CitationJournal: Sci Adv / Year: 2019
Title: Hierarchical assembly governs TRIM5α recognition of HIV-1 and retroviral capsids.
Authors: Katarzyna A Skorupka / Marcin D Roganowicz / Devin E Christensen / Yueping Wan / Owen Pornillos / Barbie K Ganser-Pornillos /
Abstract: TRIM5α is a restriction factor that senses incoming retrovirus cores through an unprecedented mechanism of nonself recognition. TRIM5α assembles a hexagonal lattice that avidly binds the capsid ...TRIM5α is a restriction factor that senses incoming retrovirus cores through an unprecedented mechanism of nonself recognition. TRIM5α assembles a hexagonal lattice that avidly binds the capsid shell, which surrounds and protects the virus core. The extent to which the TRIM lattice can cover the capsid and how TRIM5α directly contacts the capsid surface have not been established. Here, we apply cryo-electron tomography and subtomogram averaging to determine structures of TRIM5α bound to recombinant HIV-1 capsid assemblies. Our data support a mechanism of hierarchical assembly, in which a limited number of basal interaction modes are successively organized in increasingly higher-order structures that culminate in a TRIM5α cage surrounding a retroviral capsid. We further propose that cage formation explains the mechanism of restriction and provides the structural context that links capsid recognition to ubiquitin-dependent processes that disable the retrovirus.
History
DepositionAug 8, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseDec 18, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / 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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Supplemental images

emd_20574.png

Downloads & links

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Map

FileDownload / File: emd_20574.map.gz / Format: CCP4 / Size: 12.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRepresentative tomogram of a TRIM5alpha-coated HIV-1 CA tube
Voxel sizeX=Y=Z: 2.92 Å
Density
Minimum - Maximum-29514.197 - 27157.27
Average (Standard dev.)145.99261 (±4209.459)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-10981-199
Dimensions29012901401
Spacing29012901401
CellA: 8470.92 Å / B: 8470.92 Å / C: 1170.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.922.922.92
M x/y/z29012901401
origin x/y/z0.0000.0000.000
length x/y/z8470.9208470.9201170.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS1-1098-199
NC/NR/NS29012901401
D min/max/mean-29514.19727157.270145.993

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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 / NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Nanoprobes / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.0 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 reconstructionSoftware - Name: Dynamo / Number images used: 119

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