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- EMDB-47752: Structural Insights into HIV-1 Vif-Mediated Ubiquitination and De... -

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Entry
Database: EMDB / ID: EMD-47752
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*UP*GP*CP*CP*GP*GP*GP*UP*A)-3')
    • RNA: RNA (5'-R(*AP*UP*AP*CP*CP*CP*GP*GP*CP*A)-3')
    • Protein or peptide: Core-binding factor subunit beta
    • Protein or peptide: Virion infectivity factor
  • Protein or peptide: single-stranded DNA cytosine deaminase
  • 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 / 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 / negative regulation of viral genome replication / RUNX2 regulates osteoblast differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RUNX3 regulates p14-ARF / viral life cycle / cell maturation / Regulation of RUNX3 expression and activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / virion component / Transcriptional regulation of granulopoiesis / protein polyubiquitination / Regulation of RUNX2 expression and activity / osteoblast differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Estrogen-dependent gene expression / defense response to virus / sequence-specific DNA binding / transcription by RNA polymerase II / host cell cytoplasm / transcription coactivator activity / 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
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
Similarity search - Domain/homology
single-stranded DNA cytosine deaminase / Virion infectivity factor / Core-binding factor subunit beta
Similarity search - Component
Biological speciesPan troglodytes (chimpanzee) / Escherichia coli BL21(DE3) (bacteria) / Homo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 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 7, 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_47752.png

Downloads & links

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Map

FileDownload / File: emd_47752.map.gz / Format: CCP4 / Size: 216 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 384 pix.
= 311.04 Å		0.81 Å/pix.
x 384 pix.
= 311.04 Å		0.81 Å/pix.
x 384 pix.
= 311.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-0.1234445 - 21.861979000000002
Average (Standard dev.)-0.026300602 (±0.34227526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 311.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47752_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_47752_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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*UP*GP*CP*CP*GP*GP*GP*UP*A)-3')
    • RNA: RNA (5'-R(*AP*UP*AP*CP*CP*CP*GP*GP*CP*A)-3')
    • Protein or peptide: Core-binding factor subunit beta
    • Protein or peptide: Virion infectivity factor
  • Protein or peptide: single-stranded DNA cytosine deaminase
  • 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: #1-#2, #4-#5
Source (natural)Organism: Pan troglodytes (chimpanzee)

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Macromolecule #1: RNA (5'-R(P*UP*GP*CP*CP*GP*GP*GP*UP*A)-3')

MacromoleculeName: RNA (5'-R(P*UP*GP*CP*CP*GP*GP*GP*UP*A)-3') / type: rna / ID: 1 / Number of copies: 2
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 2.887767 KDa
SequenceString:
UGCCGGGUA

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

MacromoleculeName: RNA (5'-R(*AP*UP*AP*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: single-stranded DNA cytosine deaminase

MacromoleculeName: single-stranded DNA cytosine deaminase / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: single-stranded DNA cytosine deaminase
Source (natural)Organism: Pan troglodytes (chimpanzee)
Molecular weightTheoretical: 21.912309 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSMALLTAET FRLQFNNRRR LRRPYYPRKA LLCYQLTPQN GSTPTRGYFE NKKKCHAEIC FINEIKSMGL DETQCYQVTC YLTWSPCSS CAWKLVDFIQ AHDHLNLRIF ASRLYYHWCK PQQEGLRLLC GSQVPVEVMG LPEFNDCWEN FVDHEKPLSF D PCKMLEEL DKNSRAIKRR LERIKQS

UniProtKB: single-stranded DNA cytosine deaminase

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Macromolecule #4: Core-binding factor subunit beta

MacromoleculeName: Core-binding factor subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.272629 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 #5: Virion infectivity factor

MacromoleculeName: Virion infectivity factor / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: NL3-4
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 #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / 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
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: OTHER / Details: 20 mA
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: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 201593
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-9e93:
Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H

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