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- EMDB-74940: Cryo-EM structure of the dimeric HIV-2 Vif-human APOBEC3H-CBFbeta... -

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Basic information

Entry
Database: EMDB / ID: EMD-74940
TitleCryo-EM structure of the dimeric HIV-2 Vif-human APOBEC3H-CBFbeta complex
Map datasharpened map
Sample
  • Complex: HIV-2 Vif in complex with human APOBEC3H and CBFbeta
    • Protein or peptide: Virion infectivity factor
    • Protein or peptide: Core-binding factor subunit beta
    • Protein or peptide: Single-stranded DNA cytosine deaminase
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
    • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • Ligand: ZINC ION
KeywordsHIV-2 / Vif / APOBEC3H / Antagonism / Ubiquitination / ANTIVIRAL PROTEIN / ANTIVIRAL 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 / core-binding factor complex / RUNX2 regulates bone development / 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 / core-binding factor complex / RUNX2 regulates bone development / 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 / cytidine deaminase activity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / lymphocyte differentiation / RUNX2 regulates genes involved in cell migration / Transcriptional regulation by RUNX2 / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / RUNX2 regulates genes involved in differentiation of myeloid cells / myeloid cell differentiation / transposable element silencing / RUNX3 Regulates Immune Response and Cell Migration / 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 / cell maturation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of RUNX3 expression and activity / Transcriptional regulation of granulopoiesis / osteoblast differentiation / protein polyubiquitination / Regulation of RUNX2 expression and activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / transcription by RNA polymerase II / Estrogen-dependent gene expression / sequence-specific DNA binding / defense response to virus / transcription coactivator activity / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / membrane / cytoplasm
Similarity search - Function
APOBEC3H / APOBEC3H / 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 / Core-binding factor subunit beta / :
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 2 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsNiu Y / Lilly M / Ronayne EK / Emerman M / Chesarino NM / Gross JD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170792 United States
CitationJournal: Nat Commun / Year: 2026
Title: The structural mechanism of HIV-2 Vif antagonism of human APOBEC3H.
Authors: Yange Niu / Michelle Lilly / Estelle K Ronayne / Michael Emerman / Nicholas M Chesarino / John D Gross /
Abstract: Human APOBEC3 (A3) proteins restrict retrovirus infection by inducing hypermutations in viral cDNA. To counteract this restriction, lentiviruses, such as HIV-1 and HIV-2 encode the viral infectivity ...Human APOBEC3 (A3) proteins restrict retrovirus infection by inducing hypermutations in viral cDNA. To counteract this restriction, lentiviruses, such as HIV-1 and HIV-2 encode the viral infectivity factor (Vif), which hijacks a host Cullin-RING E3 ubiquitin ligase complex to target A3 proteins for proteasomal degradation. Here, we present the cryo-EM structure of HIV-2 Vif in complex with human A3H and CBFβ. The structure reveals that A3H forms a dimer mediated by dsRNA where each A3H monomer directly interacts with an HIV-2 Vif and the host protein CBFβ. Both HIV-2 Vif-A3H and CBFβ-A3H interfaces are critical for A3H degradation. Notably, however, the HIV-2 Vif-A3H interface is entirely distinct from the previously determined cryo-EM structure of the HIV-1 Vif and A3H complex. These findings suggest that HIV-1 and HIV-2 Vif, which are the result of distinct cross-species transmissions from species with different A3H characteristics, have followed separate evolutionary trajectories to counteract human A3H.
History
DepositionJan 5, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74940.png

Downloads & links

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Map

FileDownload / File: emd_74940.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 440 pix.
= 360.316 Å		0.82 Å/pix.
x 440 pix.
= 360.316 Å		0.82 Å/pix.
x 440 pix.
= 360.316 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8189 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.666119 - 2.82466
Average (Standard dev.)-0.00033362457 (±0.027751971)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 360.316 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74940_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_74940_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_74940_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-2 Vif in complex with human APOBEC3H and CBFbeta

EntireName: HIV-2 Vif in complex with human APOBEC3H and CBFbeta
Components
  • Complex: HIV-2 Vif in complex with human APOBEC3H and CBFbeta
    • Protein or peptide: Virion infectivity factor
    • Protein or peptide: Core-binding factor subunit beta
    • Protein or peptide: Single-stranded DNA cytosine deaminase
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
    • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • Ligand: ZINC ION

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Supramolecule #1: HIV-2 Vif in complex with human APOBEC3H and CBFbeta

SupramoleculeName: HIV-2 Vif in complex with human APOBEC3H and CBFbeta / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: Virion infectivity factor

MacromoleculeName: Virion infectivity factor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 2
Molecular weightTheoretical: 25.044865 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEEGKSWIVV PTWRVPGRME KWHSLVKYLK YRTKDLEKVC YVPHHKVGWA WWTCSRVIFP LQGRSHLEIQ AYWNLTPEKG WLSSYAVRI TWYTEKFWTD VTPDCADSLI HGTYFSCFTA GEVRRAIRGE KLLSCCNYPQ AHKSQVPSLQ FLALVVVQQN G KPQRNSTT ...String:
MEEGKSWIVV PTWRVPGRME KWHSLVKYLK YRTKDLEKVC YVPHHKVGWA WWTCSRVIFP LQGRSHLEIQ AYWNLTPEKG WLSSYAVRI TWYTEKFWTD VTPDCADSLI HGTYFSCFTA GEVRRAIRGE KLLSCCNYPQ AHKSQVPSLQ FLALVVVQQN G KPQRNSTT RKQWRRDYRR GLRVARQDSR GLKQRGGESP APGAHFPGVA KVLEILA

UniProtKB: UNIPROTKB: Q9YTT9

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Macromolecule #2: Core-binding factor subunit beta

MacromoleculeName: Core-binding factor subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.542188 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MPRVVPDQRS KFENEEFFRK LSRECEIKYT GFRDRPHEER QARFQNACRD GRSEIAFVAT GTNLSLQFFP ASWQGEQRQT PSREYVDLE REAGKVYLKA PMILNGVCVI WKGWIDLQRL DGMGCLEFDE ERAQQEDALA QQAFEEARRR TREFEDRDRS H REEMEVRV SQLLAVTGKK TTRP

UniProtKB: Core-binding factor subunit beta

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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: Homo sapiens (human)
Molecular weightTheoretical: 21.763137 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MALLTAETFR LQFNNKRRLR RPYYPRKALL CYQLTPQNGS TPTRGYFENK KKCHAEICFI NEIKSMGLDE TQCYQVTCYL TWSPCSSCA WELVDFIKAH DHLNLRIFAS RLYYHWCKPQ QDGLRLLCGS QVPVEVMGFP EFADCWENFV DHEKPLSFNP Y KMLEELDK NSRAIKRRLD RIKQS

UniProtKB: single-stranded DNA cytosine deaminase

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Macromolecule #4: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3') / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 2.404369 KDa
SequenceString:
UUUUUUUU

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Macromolecule #5: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3') / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 2.588689 KDa
SequenceString:
AAAAAAAA

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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

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 47.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1257210
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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