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- EMDB-47805: Structural Insights into HIV-1 Vif-Mediated Ubiquitination and De... -

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Basic information

Entry
Database: EMDB / ID: EMD-47805
TitleStructural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H
Map data
Sample
  • Complex: Ternary complex of APOBEC3H and Vif of HIV-1
    • RNA: RNA (5'-R(P*CP*CP*CP*GP*GP*CP*A)-3')
    • RNA: RNA (5'-R(P*GP*CP*CP*GP*GP*G)-3')
  • Protein or peptide: single-stranded DNA cytosine deaminase
  • Protein or peptide: Elongin-C
  • Protein or peptide: Elongin-B
  • Protein or peptide: Virion infectivity factor
  • Protein or peptide: Core-binding factor subunit beta
  • Ligand: ZINC ION
KeywordsAPOBEC3H HIV-1 Vif / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex
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 / 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 ...RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / 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 / clearance of foreign intracellular DNA / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / cytidine deaminase activity / lymphocyte differentiation / RUNX2 regulates genes involved in cell migration / Transcriptional regulation by RUNX2 / RUNX2 regulates genes involved in differentiation of myeloid cells / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / transposable element silencing / RUNX3 Regulates Immune Response and Cell Migration / myeloid cell differentiation / definitive hemopoiesis / target-directed miRNA degradation / elongin complex / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / negative regulation of viral genome replication / Cul2-RING ubiquitin ligase complex / RUNX2 regulates osteoblast differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RUNX3 regulates p14-ARF / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / viral life cycle / cell maturation / RNA Polymerase II Pre-transcription Events / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Regulation of RUNX3 expression and activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / virion component / Regulation of expression of SLITs and ROBOs / Transcriptional regulation of granulopoiesis / protein polyubiquitination / Regulation of RUNX2 expression and activity / osteoblast differentiation / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / protein-containing complex assembly / Estrogen-dependent gene expression / defense response to virus / sequence-specific DNA binding / protein-macromolecule adaptor activity / transcription by RNA polymerase II / ubiquitin-dependent protein catabolic process / host cell cytoplasm / transcription coactivator activity / protein ubiquitination / ubiquitin protein ligase binding / 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 / cytoplasm / cytosol
Similarity search - Function
APOBEC3H / APOBEC3H / 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. ...APOBEC3H / APOBEC3H / 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 / Elongin-C / Elongin B / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
single-stranded DNA cytosine deaminase / Virion infectivity factor / Core-binding factor subunit beta / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesPan troglodytes (chimpanzee) / Homo sapiens (human) / Human immunodeficiency virus 1 / Escherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsMatsuo H / Skorupka KA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 AI150478 United States
CitationJournal: Nat Commun / Year: 2025
Title: HIV-1 vif mediates ubiquitination of the proximal protomer in the APOBEC3H dimer to induce degradation.
Authors: Katarzyna A Skorupka / Kazuhiro Matsuoka / Bakar Hassan / Rodolfo Ghirlando / Vanivilasini Balachandran / Ting-Hua Chen / Kylie J Walters / Celia A Schiffer / Matthias Wolf / Yasumasa ...Authors: Katarzyna A Skorupka / Kazuhiro Matsuoka / Bakar Hassan / Rodolfo Ghirlando / Vanivilasini Balachandran / Ting-Hua Chen / Kylie J Walters / Celia A Schiffer / Matthias Wolf / Yasumasa Iwatani / Hiroshi Matsuo /
Abstract: The APOBEC3 family of cytidine deaminases restricts retroviruses like HIV-1 by mutating viral DNA. HIV-1 evades this restriction by producing Vif, which recruits the Cullin-5 (CUL5) E3 ubiquitin ...The APOBEC3 family of cytidine deaminases restricts retroviruses like HIV-1 by mutating viral DNA. HIV-1 evades this restriction by producing Vif, which recruits the Cullin-5 (CUL5) E3 ubiquitin ligase complex to promote APOBEC3 degradation. Here we resolve key aspects of this counter-defense mechanism by determining a 3.6 Å cryo-EM structure of chimpanzee APOBEC3H (cpzA3H) in complex with HIV-1 Vif and three components of the CUL5 E3 ligase-CBFβ, EloB, and EloC (VCBC). The structure captures cpzA3H as an RNA-mediated dimer within the cpzA3H-VCBC complex, allowing us to examine the role of dimerization. We find that ubiquitination occurs specifically at two lysine residues on the Vif-proximal protomer, while the distal protomer remains unmodified. The structural model of the active cpzA3H-Vif-CUL5 E3 ligase holoenzyme reveals spatial preferences for ubiquitin transfer to the targeted lysine residues. These findings enhance our understanding of A3H degradation and suggest new antiviral strategies targeting this host-virus interface.
History
DepositionNov 8, 2024-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47805.png

Downloads & links

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Map

FileDownload / File: emd_47805.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 350 pix.
= 283.5 Å		0.81 Å/pix.
x 350 pix.
= 283.5 Å		0.81 Å/pix.
x 350 pix.
= 283.5 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-0.11048868 - 14.278275499999999
Average (Standard dev.)-0.015641227 (±0.38942674)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 283.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47805_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_47805_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of APOBEC3H and Vif of HIV-1

EntireName: Ternary complex of APOBEC3H and Vif of HIV-1
Components
  • Complex: Ternary complex of APOBEC3H and Vif of HIV-1
    • RNA: RNA (5'-R(P*CP*CP*CP*GP*GP*CP*A)-3')
    • RNA: RNA (5'-R(P*GP*CP*CP*GP*GP*G)-3')
  • Protein or peptide: single-stranded DNA cytosine deaminase
  • Protein or peptide: Elongin-C
  • Protein or peptide: Elongin-B
  • Protein or peptide: Virion infectivity factor
  • Protein or peptide: Core-binding factor subunit beta
  • Ligand: ZINC ION

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Supramolecule #1: Ternary complex of APOBEC3H and Vif of HIV-1

SupramoleculeName: Ternary complex of APOBEC3H and Vif of HIV-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3
Source (natural)Organism: Pan troglodytes (chimpanzee)

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Macromolecule #1: single-stranded DNA cytosine deaminase

MacromoleculeName: single-stranded DNA cytosine deaminase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: single-stranded DNA cytosine deaminase
Source (natural)Organism: Pan troglodytes (chimpanzee)
Molecular weightTheoretical: 21.76818 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MALLTAETFR LQFNNRRRLR RPYYPRKALL CYQLTPQNGS TPTRGYFENK KKCHAEICFI NEIKSMGLDE TQCYQVTCYL TWSPCSSCA WKLVDFIQAH DHLNLRIFAS RLYYHWCKPQ QEGLRLLCGS QVPVEVMGLP EFNDCWENFV DHEKPLSFDP C KMLEELDK NSRAIKRRLE RIKQS

UniProtKB: single-stranded DNA cytosine deaminase

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Macromolecule #4: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.84342 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MYVKLISSDG HEFIVKREHA LTSGTIKAML SGPGQFAENE TNEVNFREIP SHVLSKVCMY FTYKVRYTNS STEIPEFPIA PEIALELLM AANFLDC

UniProtKB: Elongin-C

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Macromolecule #5: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.48803 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDV

UniProtKB: Elongin-B

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Macromolecule #6: Virion infectivity factor

MacromoleculeName: Virion infectivity factor / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 20.98224 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MENRWQVMIV WQVDRMRINT WKRLVKHHMY ISRKAKDWFY RHHYESTNPK ISSEVHIPLG DAKLVITTYW GLHTGERDWH LGQGVSIEW RKKRYSTQVD PDLADQLIHL HYFDCFSESA IRNTILGRIV SPRCEYQAGH NKVGSLQYLA LAALIKPKQI K PPLPSVRK LTEDRWNK

UniProtKB: Virion infectivity factor

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Macromolecule #7: Core-binding factor subunit beta

MacromoleculeName: Core-binding factor subunit beta / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.272629 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MPRVVPDQRS KFENEEFFRK LSRECEIKYT GFRDRPHEER QARFQNACRD GRSEIAFVAT GTNLSLQFFP ASWQGEQRQT PSREYVDLE REAGKVYLKA PMILNGVCVI WKGWIDLQRL DGMGCLEFDE ERAQQEDALA QQAFEEARRR TREFEDRDRS H REEMEVRV SQ

UniProtKB: Core-binding factor subunit beta

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Macromolecule #2: RNA (5'-R(P*CP*CP*CP*GP*GP*CP*A)-3')

MacromoleculeName: RNA (5'-R(P*CP*CP*CP*GP*GP*CP*A)-3') / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 3.159965 KDa
SequenceString:
AUACCCGGCA

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Macromolecule #3: RNA (5'-R(P*GP*CP*CP*GP*GP*G)-3')

MacromoleculeName: RNA (5'-R(P*GP*CP*CP*GP*GP*G)-3') / type: rna / ID: 3 / Number of copies: 2
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 2.887767 KDa
SequenceString:
UGCCGGGUA

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 4 / 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

Concentration0.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
200.0 mMNaClsodium chloride
1.0 mMTCEP
0.25 %glycerol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Number real images: 44142 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 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 / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5z98

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 215818
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4n9z

chain_id: m, source_name: PDB, initial_model_type: experimental model

4n9z

chain_id: n, source_name: PDB, initial_model_type: experimental model

4n9z

chain_id: o, source_name: PDB, initial_model_type: experimental model

4n9z

chain_id: p, source_name: PDB, initial_model_type: experimental model

5z98

chain_id: A, source_name: PDB, initial_model_type: experimental model

5z98

chain_id: B, source_name: PDB, initial_model_type: experimental model

5z98

chain_id: C, source_name: PDB, initial_model_type: experimental model

5z98

chain_id: D, source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT / Overall B value: 135
Output model

PDB-9e9v:
Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H

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