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- EMDB-27875: Full-length APOBEC3G in complex with HIV-1 Vif, CBF-beta, and fork RNA -

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Basic information

Entry
Database: EMDB / ID: EMD-27875
TitleFull-length APOBEC3G in complex with HIV-1 Vif, CBF-beta, and fork RNA
Map data
Sample
  • Complex: Complex of APOBEC3G with HIV-1 Vif and CBF-beta bound to fork RNA
    • Protein or peptide: DNA dC->dU-editing enzyme APOBEC-3G
    • Protein or peptide: Virion infectivity factor
    • Protein or peptide: Core-binding factor subunit beta
    • RNA: RNA
    • RNA: RNA
  • Ligand: ZINC ION
Function / homology
Function and homology information


: / RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / cytidine deamination / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation ...: / RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / cytidine deamination / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / single-stranded DNA cytosine deaminase / negative regulation of CD4-positive, alpha-beta T cell differentiation / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / lymphocyte differentiation / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX2 regulates genes involved in cell migration / RUNX2 regulates genes involved in differentiation of myeloid cells / Transcriptional regulation by RUNX2 / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / myeloid cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / definitive hemopoiesis / DNA demethylation / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RUNX2 regulates osteoblast differentiation / RUNX3 regulates p14-ARF / cell maturation / viral life cycle / virion component / P-body / Regulation of RUNX3 expression and activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / osteoblast differentiation / protein polyubiquitination / Transcriptional regulation of granulopoiesis / Regulation of RUNX2 expression and activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / defense response to virus / Estrogen-dependent gene expression / host cell cytoplasm / sequence-specific DNA binding / transcription by RNA polymerase II / transcription coactivator activity / ribonucleoprotein complex / innate immune response / regulation of transcription by RNA polymerase II / host cell plasma membrane / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
DNA dC->dU-editing enzyme APOBEC-3G / Retroviral Vif (Viral infectivity) protein / Retroviral Vif (Viral infectivity) protein / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily / Core binding factor beta subunit / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
Virion infectivity factor / Core-binding factor subunit beta / DNA dC->dU-editing enzyme APOBEC-3G
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey) / Homo sapiens (human) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 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 17, 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

Downloads & links

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Map

FileDownload / File: emd_27875.map.gz / Format: CCP4 / Size: 216 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-0.19147603 - 0.554517
Average (Standard dev.)2.6490732e-05 (±0.007658874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27875_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_27875_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Complex of APOBEC3G with HIV-1 Vif and CBF-beta bound to fork RNA

EntireName: Complex of APOBEC3G with HIV-1 Vif and CBF-beta bound to fork RNA
Components
  • Complex: Complex of APOBEC3G with HIV-1 Vif and CBF-beta bound to fork RNA
    • Protein or peptide: DNA dC->dU-editing enzyme APOBEC-3G
    • Protein or peptide: Virion infectivity factor
    • Protein or peptide: Core-binding factor subunit beta
    • RNA: RNA
    • RNA: RNA
  • Ligand: ZINC ION

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Supramolecule #1: Complex of APOBEC3G with HIV-1 Vif and CBF-beta bound to fork RNA

SupramoleculeName: Complex of APOBEC3G with HIV-1 Vif and CBF-beta bound to fork RNA
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 99 KDa

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Macromolecule #1: DNA dC->dU-editing enzyme APOBEC-3G

MacromoleculeName: DNA dC->dU-editing enzyme APOBEC-3G / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: single-stranded DNA cytosine deaminase
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 45.18743 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGGSGGMKP QIRNMVEPMD PRTFVSNFNN RPILSGLDTV WLCCEVKTKD PSGPPLDAKI FQGKVYPKAK YHPEMRFLRW FHKWRQLHH DQEYKVTWYV SWSPCTRCAN SVATFLAKDP KVTLTIFVAR LYYFWDPDYQ QALRILAEAG ATMKIMNYNE F QDCWNKFV ...String:
GPGGSGGMKP QIRNMVEPMD PRTFVSNFNN RPILSGLDTV WLCCEVKTKD PSGPPLDAKI FQGKVYPKAK YHPEMRFLRW FHKWRQLHH DQEYKVTWYV SWSPCTRCAN SVATFLAKDP KVTLTIFVAR LYYFWDPDYQ QALRILAEAG ATMKIMNYNE F QDCWNKFV DGRGKPFKPW NNLPKHYTLL QATLGELLRH LMDPGTFTSN FNNKPWVSGQ HETYLCYKVE RLHNDTWVPL NQ HRGFLRN QAPNIHGFPK GRHAQLCFLD LIPFWKLDGQ QYRVTCFTSW SPCFSCAQEM AKFISNNEHV SLCIFAARIY DDQ GRYQEG LRTLHRDGAK IAMMNYSEFE YCWDTFVDRQ GRPFQPWDGL DEHSQALSGR LRAILQNQGN

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Macromolecule #2: Virion infectivity factor

MacromoleculeName: Virion infectivity factor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 21.136408 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPMENRWQVM IVWQVDRMRI NTWKRLVKHH MYISRKAKDW FYRHHYESTN PKISSEVHIP LGDAKLVITT YWGLHTGERD WHLGQGVSI EWRKKRYSTQ VDPDLADQLI HLHYFDCFSE SAIRNTILGR IVSPRCEYQA GHNKVGSLQY LALAALIKPK Q IKPPLPSV RKLTEDRWNK

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Macromolecule #3: Core-binding factor subunit beta

MacromoleculeName: Core-binding factor subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.643814 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPRVVPDQRS KFENEEFFRK LSRECEIKYT GFRDRPHEER QARFQNACRD GRSEIAFVAT GTNLSLQFFP ASWQGEQRQT PSREYVDLE REAGKVYLKA PMILNGVCVI WKGWIDLQRL DGMGCLEFDE ERAQQEDALA QQAFEEARRR TREFEDRD

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Macromolecule #4: RNA

MacromoleculeName: RNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 6.875011 KDa
SequenceString:
UUUUUUUUUU UUUUAAAAAA AA

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Macromolecule #5: RNA

MacromoleculeName: RNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.00087 KDa
SequenceString:
UUUUUUUUAA AAAAAAAAAA AAAAA

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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
GridModel: Quantifoil
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

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
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 432841
FSC plot (resolution estimation)

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