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- EMDB-9381: CryoEM reconstruction of the full HIV-1 Vif/CBFbeta/A3F complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9381
TitleCryoEM reconstruction of the full HIV-1 Vif/CBFbeta/A3F complex
Map dataprimary map
Sample
  • Complex: Vif/CBFbeta/A3Fctd complex
    • Complex: APOBEC3F C-terminal domain (hA3Fctd)
      • Protein or peptide: human APOBEC3F C-terminal domain (hA3Fctd)
    • Complex: core-binding factor beta (CBFbeta)
      • Protein or peptide: human core-binding factor beta (CBFbeta)
    • Complex: HIV-1 virion infectivity factor (Vif)
      • Protein or peptide: HIV-1 virion infectivity factor (Vif)
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsHu Y / Xiong Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research ResourcesAI116313 United States
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Structural basis of antagonism of human APOBEC3F by HIV-1 Vif.
Authors: Yingxia Hu / Belete A Desimmie / Henry C Nguyen / Samantha J Ziegler / Tat Cheung Cheng / John Chen / Jia Wang / Hongwei Wang / Kai Zhang / Vinay K Pathak / Yong Xiong /
Abstract: HIV-1 virion infectivity factor (Vif) promotes degradation of the antiviral APOBEC3 (A3) proteins through the host ubiquitin-proteasome pathway to enable viral immune evasion. Disrupting Vif-A3 ...HIV-1 virion infectivity factor (Vif) promotes degradation of the antiviral APOBEC3 (A3) proteins through the host ubiquitin-proteasome pathway to enable viral immune evasion. Disrupting Vif-A3 interactions to reinstate the A3-catalyzed suppression of human immunodeficiency virus type 1 (HIV-1) replication is a potential approach for antiviral therapeutics. However, the molecular mechanisms by which Vif recognizes A3 proteins remain elusive. Here we report a cryo-EM structure of the Vif-targeted C-terminal domain of human A3F in complex with HIV-1 Vif and the cellular cofactor core-binding factor beta (CBFβ) at 3.9-Å resolution. The structure shows that Vif and CBFβ form a platform to recruit A3F, revealing a direct A3F-recruiting role of CBFβ beyond Vif stabilization, and captures multiple independent A3F-Vif interfaces. Together with our biochemical and cellular studies, our structural findings establish the molecular determinants that are critical for Vif-mediated neutralization of A3F and provide a comprehensive framework of how HIV-1 Vif hijacks the host protein degradation machinery to counteract viral restriction by A3F.
History
DepositionDec 29, 2018-
Header (metadata) releaseDec 11, 2019-
Map releaseDec 11, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9381.png

Downloads & links

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Map

FileDownload / File: emd_9381.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 224 pix.
= 235.2 Å		1.05 Å/pix.
x 224 pix.
= 235.2 Å		1.05 Å/pix.
x 224 pix.
= 235.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.039340224 - 0.11030433
Average (Standard dev.)0.00080856006 (±0.00531041)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 235.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z235.200235.200235.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0390.1100.001

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Supplemental data

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Sample components

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Entire : Vif/CBFbeta/A3Fctd complex

EntireName: Vif/CBFbeta/A3Fctd complex
Components
  • Complex: Vif/CBFbeta/A3Fctd complex
    • Complex: APOBEC3F C-terminal domain (hA3Fctd)
      • Protein or peptide: human APOBEC3F C-terminal domain (hA3Fctd)
    • Complex: core-binding factor beta (CBFbeta)
      • Protein or peptide: human core-binding factor beta (CBFbeta)
    • Complex: HIV-1 virion infectivity factor (Vif)
      • Protein or peptide: HIV-1 virion infectivity factor (Vif)

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Supramolecule #1: Vif/CBFbeta/A3Fctd complex

SupramoleculeName: Vif/CBFbeta/A3Fctd complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 250 KDa

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Supramolecule #2: APOBEC3F C-terminal domain (hA3Fctd)

SupramoleculeName: APOBEC3F C-terminal domain (hA3Fctd) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: core-binding factor beta (CBFbeta)

SupramoleculeName: core-binding factor beta (CBFbeta) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: HIV-1 virion infectivity factor (Vif)

SupramoleculeName: HIV-1 virion infectivity factor (Vif) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: human APOBEC3F C-terminal domain (hA3Fctd)

MacromoleculeName: human APOBEC3F C-terminal domain (hA3Fctd) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPNSMGKE ILRNPMEAMD PHIFYFHFKN LRKAYGRNES WLCFTMEVVK HHSPVSWKRG VFRNQVDPET GRHAERCFLS WFCDDILSPN TNYEVTWYTS WSPCPECAGE VAEFLARHSN VNLTIKTARL YYFKDTDAAE GLRSLSQEGA SVEIMGYKDF ...String:
MGSSHHHHHH SQDPNSMGKE ILRNPMEAMD PHIFYFHFKN LRKAYGRNES WLCFTMEVVK HHSPVSWKRG VFRNQVDPET GRHAERCFLS WFCDDILSPN TNYEVTWYTS WSPCPECAGE VAEFLARHSN VNLTIKTARL YYFKDTDAAE GLRSLSQEGA SVEIMGYKDF KYCWENFVYN DDEPFKPWDG LDYNFLDLDS KLQEILE

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Macromolecule #2: human core-binding factor beta (CBFbeta)

MacromoleculeName: human core-binding factor beta (CBFbeta) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPRVVPDQRS KFENEEFFRK LSRECEIKYT GFRDRPHEER QARFQNACRD GRSEIAFVAT GTNLSLQFFP ASWQGEQRQT PSREYVDLER EAGKVYLKAP MILNGVCVIW KGWIDLQRLD GMGCLEFDEE RAQQEDALAQ QAFEEARRRT REFEDRDRSH REEMEARRQQ DPSPGSNLGG GDDLKLR

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Macromolecule #3: HIV-1 virion infectivity factor (Vif)

MacromoleculeName: HIV-1 virion infectivity factor (Vif) / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MENRWQVMIV WQVDRMRINT WKRLVKHHMY ISRKAKDWFY RHHYESTNPK ISSEVHIPLG DAKLVITTYW GLHTGERDWH LGQGVSIEWR KKRYSTQVDP DLADQLIHLH YFDCFSESAI RNTILGRIVS PRCEYQAGHN KVGSLQYLAL AALIKPKQIK PPLPSVRKLT EDRWNK

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 165629
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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