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- EMDB-22410: Cryo-electron tomography of HIV-1 integrase mutant, W235E -

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Entry
Database: EMDB / ID: EMD-22410
TitleCryo-electron tomography of HIV-1 integrase mutant, W235E
Map dataCryo-electron tomography of HIV-1 integrase mutant, W235E
Sample
  • Virus: Human immunodeficiency virus 1
Biological speciesHuman immunodeficiency virus 1
Methodelectron tomography / cryo EM
AuthorsAdams LJ / Steven AC
CitationJournal: Nat Commun / Year: 2021
Title: INI1/SMARCB1 Rpt1 domain mimics TAR RNA in binding to integrase to facilitate HIV-1 replication.
Authors: Updesh Dixit / Savita Bhutoria / Xuhong Wu / Liming Qiu / Menachem Spira / Sheeba Mathew / Richard Harris / Lucas J Adams / Sean Cahill / Rajiv Pathak / P Rajesh Kumar / Minh Nguyen / ...Authors: Updesh Dixit / Savita Bhutoria / Xuhong Wu / Liming Qiu / Menachem Spira / Sheeba Mathew / Richard Harris / Lucas J Adams / Sean Cahill / Rajiv Pathak / P Rajesh Kumar / Minh Nguyen / Seetharama A Acharya / Michael Brenowitz / Steven C Almo / Xiaoqin Zou / Alasdair C Steven / David Cowburn / Mark Girvin / Ganjam V Kalpana /
Abstract: INI1/SMARCB1 binds to HIV-1 integrase (IN) through its Rpt1 domain and exhibits multifaceted role in HIV-1 replication. Determining the NMR structure of INI1-Rpt1 and modeling its interaction with ...INI1/SMARCB1 binds to HIV-1 integrase (IN) through its Rpt1 domain and exhibits multifaceted role in HIV-1 replication. Determining the NMR structure of INI1-Rpt1 and modeling its interaction with the IN-C-terminal domain (IN-CTD) reveal that INI1-Rpt1/IN-CTD interface residues overlap with those required for IN/RNA interaction. Mutational analyses validate our model and indicate that the same IN residues are involved in both INI1 and RNA binding. INI1-Rpt1 and TAR RNA compete with each other for IN binding with similar IC values. INI1-interaction-defective IN mutant viruses are impaired for incorporation of INI1 into virions and for particle morphogenesis. Computational modeling of IN-CTD/TAR complex indicates that the TAR interface phosphates overlap with negatively charged surface residues of INI1-Rpt1 in three-dimensional space, suggesting that INI1-Rpt1 domain structurally mimics TAR. This possible mimicry between INI1-Rpt1 and TAR explains the mechanism by which INI1/SMARCB1 influences HIV-1 late events and suggests additional strategies to inhibit HIV-1 replication.
History
DepositionAug 7, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing 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_22410.png

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Map

FileDownload / File: emd_22410.map.gz / Format: CCP4 / Size: 8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomography of HIV-1 integrase mutant, W235E
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.32 Å/pix.
x 600 pix.
= 4392. Å		7.32 Å/pix.
x 1919 pix.
= 14047.08 Å		7.32 Å/pix.
x 1855 pix.
= 13578.601 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: 7.32 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-38.631252 - 24.201422
Average (Standard dev.)4.3123193e-13 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-959-926-299
Dimensions19191855600
Spacing18551919600
CellA: 13578.601 Å / B: 14047.08 Å / C: 4392.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.32000053908367.327.32
M x/y/z18551919600
origin x/y/z0.0000.0000.000
length x/y/z13578.60114047.0804392.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-926-959-299
NC/NR/NS18551919600
D min/max/mean-38.63124.2010.000

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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: HIV-1 virions were generated via transient transfection of 293T cells.
NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Sci species strain: NL4-3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
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
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Electron Microscopy Sciences / Diameter: 10 nm

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Electron microscopy

MicroscopeJEOL 2200FS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionSoftware - Name: Bsoft / Number images used: 56

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