National Institutes of Health/National Institute of General Medical Sciences
R01-GM112508
United States
National Institutes of Health/National Institute of General Medical Sciences
P50-GM082545
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases
R01-AI150479
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases
P50-AI150464
United States
Citation
Journal: 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
Deposition
Aug 6, 2019
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Header (metadata) release
Aug 28, 2019
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Map release
Dec 18, 2019
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Update
Dec 18, 2019
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Current status
Dec 18, 2019
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_20565.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
TRIM5alpha lattice bound to HIV-1 capsid lattice
Voxel size
X=Y=Z: 5.84 Å
Density
Contour Level
By AUTHOR: 2 / Movie #1: 2
Minimum - Maximum
-21.533178 - 20.61271
Average (Standard dev.)
-0.018860996 (±1.4090933)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
96
96
96
Spacing
96
96
96
Cell
A=B=C: 560.64 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
5.84
5.84
5.84
M x/y/z
96
96
96
origin x/y/z
0.000
0.000
0.000
length x/y/z
560.640
560.640
560.640
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
96
96
96
D min/max/mean
-21.533
20.613
-0.019
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Supplemental data
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Sample components
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Entire : Human immunodeficiency virus 1
Entire
Name: Human immunodeficiency virus 1
Components
Virus: Human immunodeficiency virus 1
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Supramolecule #1: Human immunodeficiency virus 1
Supramolecule
Name: 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 system
Organism: Escherichia coli (E. coli)
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Experimental details
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Structure determination
Method
cryo EM
Processing
subtomogram averaging
Aggregation state
helical array
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Sample preparation
Buffer
pH: 8
Vitrification
Cryogen name: ETHANE
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Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics
Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
Final reconstruction
Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: OTHER / Software - Name: Dynamo / Number subtomograms used: 335
Extraction
Number tomograms: 7 / Number images used: 10555 / Software - Name: Dynamo
Final angle assignment
Type: ANGULAR RECONSTITUTION
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