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- EMDB-27887: RNA-mediated APOBEC3G dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-27887
TitleRNA-mediated APOBEC3G dimer
Map data
Sample
  • Complex: APOBEC3G dimer mediated by RNA
    • Protein or peptide: APOBEC3G
Biological speciesMacaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsIto F / Alvarez-Cabrera AL / Liu S / Yang H / Shiriaeva A / Zhou ZH / Chen XS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI150524 United States
CitationJournal: Sci Adv / Year: 2023
Title: Structural basis for HIV-1 antagonism of host APOBEC3G via Cullin E3 ligase.
Authors: Fumiaki Ito / Ana L Alvarez-Cabrera / Shiheng Liu / Hanjing Yang / Anna Shiriaeva / Z Hong Zhou / Xiaojiang S Chen /
Abstract: Human APOBEC3G (A3G) is a virus restriction factor that inhibits HIV-1 replication and triggers lethal hypermutation on viral reverse transcripts. HIV-1 viral infectivity factor (Vif) breaches this ...Human APOBEC3G (A3G) is a virus restriction factor that inhibits HIV-1 replication and triggers lethal hypermutation on viral reverse transcripts. HIV-1 viral infectivity factor (Vif) breaches this host A3G immunity by hijacking a cellular E3 ubiquitin ligase complex to target A3G for ubiquitination and degradation. The molecular mechanism of A3G targeting by Vif-E3 ligase is unknown, limiting the antiviral efforts targeting this host-pathogen interaction crucial for HIV-1 infection. Here, we report the cryo-electron microscopy structures of A3G bound to HIV-1 Vif in complex with T cell transcription cofactor CBF-β and multiple components of the Cullin-5 RING E3 ubiquitin ligase. The structures reveal unexpected RNA-mediated interactions of Vif with A3G primarily through A3G's noncatalytic domain, while A3G's catalytic domain is poised for ubiquitin transfer. These structures elucidate the molecular mechanism by which HIV-1 Vif hijacks the host ubiquitin ligase to specifically target A3G to establish infection and offer structural information for the rational development of antiretroviral therapeutics.
History
DepositionAug 18, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJan 11, 2023-
Current statusJan 11, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27887.png

Downloads & links

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Map

FileDownload / File: emd_27887.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.92 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.1483165 - 0.3053233
Average (Standard dev.)-1.6005648e-05 (±0.00570475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 471.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27887_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27887_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : APOBEC3G dimer mediated by RNA

EntireName: APOBEC3G dimer mediated by RNA
Components
  • Complex: APOBEC3G dimer mediated by RNA
    • Protein or peptide: APOBEC3G

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Supramolecule #1: APOBEC3G dimer mediated by RNA

SupramoleculeName: APOBEC3G dimer mediated by RNA / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 108 KDa

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Macromolecule #1: APOBEC3G

MacromoleculeName: APOBEC3G / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGGSGGMKP QIRNMVEPMD PRTFVSNFNN RPILSGLDTV WLCCEVKTKD PSGPPLDAKI FQGKVYPKAK YHPEMRFLRW FHKWRQLHHD QEYKVTWYVS WSPCTRCANS VATFLAKDPK VTLTIFVARL YYFWDPDYQQ ALRILAEAGA TMKIMNYNEF QDCWNKFVDG ...String:
GPGGSGGMKP QIRNMVEPMD PRTFVSNFNN RPILSGLDTV WLCCEVKTKD PSGPPLDAKI FQGKVYPKAK YHPEMRFLRW FHKWRQLHHD QEYKVTWYVS WSPCTRCANS VATFLAKDPK VTLTIFVARL YYFWDPDYQQ ALRILAEAGA TMKIMNYNEF QDCWNKFVDG RGKPFKPWNN LPKHYTLLQA TLGELLRHLM DPGTFTSNFN NKPWVSGQHE TYLCYKVERL HNDTWVPLNQ HRGFLRNQAP NIHGFPKGRH AQLCFLDLIP FWKLDGQQYR VTCFTSWSPC FSCAQEMAKF ISNNEHVSLC IFAARIYDDQ GRYQEGLRTL HRDGAKIAMM NYSEFEYCWD TFVDRQGRPF QPWDGLDEHS QALSGRLRAI LQNQGN

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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

Concentration0.15 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 150000
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 11803 / Average exposure time: 8.0 sec. / Average electron dose: 40.0 e/Å2

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Image processing

Particle selectionNumber selected: 5032127
Startup modelType of model: INSILICO MODEL
In silico model: Generated by stochastic gradient descent using ab intio reconstruction in cryoSPARC.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 116460
FSC plot (resolution estimation)

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