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- EMDB-20563: TRIM5alpha dimer in complex with HIV-1 capsid tubes -

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Basic information

Entry
Database: EMDB / ID: EMD-20563
TitleTRIM5alpha dimer in complex with HIV-1 capsid tubes
Map dataTRIM5alpha dimer
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 6, 2019-
Header (metadata) releaseAug 28, 2019-
Map releaseDec 18, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20563.png

Downloads & links

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Map

FileDownload / File: emd_20563.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRIM5alpha dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.92 Å/pix.
x 128 pix.
= 373.76 Å		2.92 Å/pix.
x 128 pix.
= 373.76 Å		2.92 Å/pix.
x 128 pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelMovie #1: 2
Minimum - Maximum-16.172056 - 22.750994
Average (Standard dev.)-0.010374953 (±1.0537183)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.922.922.92
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z373.760373.760373.760
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-16.17222.751-0.010

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Supplemental data

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Half map: TRIM5alpha dimer odd half-set

Fileemd_20563_half_map_1.map
AnnotationTRIM5alpha dimer odd half-set
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TRIM5alpha dimer even half-set

Fileemd_20563_half_map_2.map
AnnotationTRIM5alpha dimer even half-set
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
FSC plot (resolution estimation)

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