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- EMDB-29490: HIV-1 Vif in complex with human APOBEC3H, CBF-beta, ELOB, ELOC, C... -

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Entry
Database: EMDB / ID: EMD-29490
TitleHIV-1 Vif in complex with human APOBEC3H, CBF-beta, ELOB, ELOC, CUL5, and RBX2
Map data
Sample
  • Complex: Hetero-heptameric complex of HIV-1 Vif and human APOBEC3H, CBF-beta, ELOB, ELOC, CUL5, and RBX2
    • Protein or peptide: Core-binding factor subunit beta
    • Protein or peptide: Virion infectivity factor
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: Cullin-5
    • Protein or peptide: RING-box protein 2
    • Protein or peptide: DNA dC->dU-editing enzyme APOBEC-3H
Keywordsvirus-host protein complex / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / mRNA Editing: C to U Conversion / Formation of the Editosome / 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 ...RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / mRNA Editing: C to U Conversion / Formation of the Editosome / 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 / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA cytosine deamination / cytidine to uridine editing / host-mediated suppression of viral genome replication / clearance of foreign intracellular DNA / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / lymphocyte differentiation / ERBB2 signaling pathway / cytidine deaminase activity / 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 / reelin-mediated signaling pathway / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / myeloid cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / regulation of neuron migration / definitive hemopoiesis / target-directed miRNA degradation / elongin complex / protein K11-linked ubiquitination / protein neddylation / Regulation of RUNX1 Expression and Activity / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / NEDD8 ligase activity / VCB complex / response to redox state / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / Cul2-RING ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / RUNX2 regulates osteoblast differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / site of DNA damage / cullin family protein binding / 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 / endoplasmic reticulum unfolded protein response / Formation of HIV elongation complex in the absence of HIV Tat / cell maturation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / viral life cycle / RNA Polymerase II Pre-transcription Events / intrinsic apoptotic signaling pathway / post-translational protein modification / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / Regulation of RUNX3 expression and activity / G1/S transition of mitotic cell cycle / Vif-mediated degradation of APOBEC3G / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RING-type E3 ubiquitin transferase / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / virion component / calcium channel activity / Downregulation of ERBB2 signaling / Regulation of expression of SLITs and ROBOs / Transcriptional regulation of granulopoiesis / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / osteoblast differentiation / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / signaling receptor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity
Similarity search - Function
APOBEC3H / APOBEC3 / 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 / APOBEC3 / 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. / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Elongin-C / Elongin B / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / Cullin family profile. / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Virion infectivity factor / Core-binding factor subunit beta / Elongin-C / Elongin-B / DNA dC->dU-editing enzyme APOBEC-3H / Cullin-5 / RING-box protein 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 5.14 Å
AuthorsIto F / Alvarez-Cabrera AL / Zhou ZH / Chen XS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI150524 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis of HIV-1 Vif-mediated E3 ligase targeting of host APOBEC3H.
Authors: Fumiaki Ito / Ana L Alvarez-Cabrera / Kyumin Kim / Z Hong Zhou / Xiaojiang S Chen /
Abstract: Human APOBEC3 (A3) cytidine deaminases are antiviral factors that are particularly potent against retroviruses. As a countermeasure, HIV-1 uses a viral infectivity factor (Vif) to target specific ...Human APOBEC3 (A3) cytidine deaminases are antiviral factors that are particularly potent against retroviruses. As a countermeasure, HIV-1 uses a viral infectivity factor (Vif) to target specific human A3s for proteasomal degradation. Vif recruits cellular transcription cofactor CBF-β and Cullin-5 (CUL5) RING E3 ubiquitin ligase to bind different A3s distinctively, but how this is accomplished remains unclear in the absence of the atomic structure of the complex. Here, we present the cryo-EM structures of HIV-1 Vif in complex with human A3H, CBF-β and components of CUL5 ubiquitin ligase (CUL5, ELOB, and ELOC). Vif nucleates the entire complex by directly binding four human proteins, A3H, CBF-β, CUL5, and ELOC. The structures reveal a large interface area between A3H and Vif, primarily mediated by an α-helical side of A3H and a five-stranded β-sheet of Vif. This A3H-Vif interface unveils the basis for sensitivity-modulating polymorphism of both proteins, including a previously reported gain-of-function mutation in Vif isolated from HIV/AIDS patients. Our structural and functional results provide insights into the remarkable interplay between HIV and humans and would inform development efforts for anti-HIV therapeutics.
History
DepositionJan 19, 2023-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29490.png

Downloads & links

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Map

FileDownload / File: emd_29490.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 512 pix.
= 471.04 Å		0.92 Å/pix.
x 512 pix.
= 471.04 Å		0.92 Å/pix.
x 512 pix.
= 471.04 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.16860732 - 0.28133452
Average (Standard dev.)-0.000096425705 (±0.005696302)
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: #1

Fileemd_29490_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29490_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Hetero-heptameric complex of HIV-1 Vif and human APOBEC3H, CBF-be...

EntireName: Hetero-heptameric complex of HIV-1 Vif and human APOBEC3H, CBF-beta, ELOB, ELOC, CUL5, and RBX2
Components
  • Complex: Hetero-heptameric complex of HIV-1 Vif and human APOBEC3H, CBF-beta, ELOB, ELOC, CUL5, and RBX2
    • Protein or peptide: Core-binding factor subunit beta
    • Protein or peptide: Virion infectivity factor
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: Cullin-5
    • Protein or peptide: RING-box protein 2
    • Protein or peptide: DNA dC->dU-editing enzyme APOBEC-3H

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Supramolecule #1: Hetero-heptameric complex of HIV-1 Vif and human APOBEC3H, CBF-be...

SupramoleculeName: Hetero-heptameric complex of HIV-1 Vif and human APOBEC3H, CBF-beta, ELOB, ELOC, CUL5, and RBX2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Core-binding factor subunit beta

MacromoleculeName: Core-binding factor subunit beta / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPRVVPDQRS KFENEEFFR K LSRECEIK YT GFRDRPH EER QARFQN ACRD GRSEI AFVAT GTNL SLQFFP ASW QGEQRQT PS REYVDLER E AGKVYLKAP MILNGVCVIW KGWIDLQRL D GMGCLEFD EE RAQQEDA LAQ QAFEEA RRRT REFED RD

UniProtKB: Core-binding factor subunit beta

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Macromolecule #2: Virion infectivity factor

MacromoleculeName: Virion infectivity factor / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: pNL4-3
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPMENRWQVM IV WQVDRMR INT WKRLVK HHMY ISRKA KDWFY RHHY ESTHPK ISS EVHIPLG DA KLVITTYW G LHTGERDWH LGQGVSIEWR KKRYSTQVD P DLADQLIH LH YFDCFSE SAI RNTILG RIVS PRCEY QAGHN KVGS LQYLAL AAL ...String:
GPMENRWQVM IV WQVDRMR INT WKRLVK HHMY ISRKA KDWFY RHHY ESTHPK ISS EVHIPLG DA KLVITTYW G LHTGERDWH LGQGVSIEWR KKRYSTQVD P DLADQLIH LH YFDCFSE SAI RNTILG RIVS PRCEY QAGHN KVGS LQYLAL AAL IKPKQIK PP LPSVRKLT E DRWNK

UniProtKB: Virion infectivity factor

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Macromolecule #3: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDVFLMIRRH KTTIFTDAK E SSTVFELK RI VEGILKR PPD EQRLYK DDQL LDDGK TLGEC GFTS QTARPQ APA TVGLAFR AD DTFEALCI E PFSSPPELP DV

UniProtKB: Elongin-B

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Macromolecule #4: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MYVKLISSDG HEFIVKREH A LTSGTIKA ML SGPGQFA ENE TNEVNF REIP SHVLS KVCMY FTYK VRYTNS STE IPEFPIA PE IALELLMA A NFLDC

UniProtKB: Elongin-C

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Macromolecule #5: Cullin-5

MacromoleculeName: Cullin-5 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SLQFEDKWD FMRPIVLKLL RQESVTKQQ W FDLFSDVH AV CLWDDKG PAK IHQALK EDIL EFIKQ AQARV LSHQ DDTALL KAY IVEWRKF FT QCDILPKP F CQLEITLMG KQGSNKKSNV EDSIVRKLM L DTWNESIF SN IKNRLQD SAM KLVHAE RLGE ...String:
SLQFEDKWD FMRPIVLKLL RQESVTKQQ W FDLFSDVH AV CLWDDKG PAK IHQALK EDIL EFIKQ AQARV LSHQ DDTALL KAY IVEWRKF FT QCDILPKP F CQLEITLMG KQGSNKKSNV EDSIVRKLM L DTWNESIF SN IKNRLQD SAM KLVHAE RLGE AFDSQ LVIGV RESY VNLCSN PED KLQIYRD NF EKAYLDST E RFYRTQAPS YLQQNGVQNY MKYADAKLK E EEKRALRY LE TRRECNS VEA LMECCV NALV TSFKE TILAE CQGM IKRNET EKL HLMFSLM DK VPNGIEPM L KDLEEHIIS AGLADMVAAA ETITTDSEK Y VEQLLTLF NR FSKLVKE AFQ DDPRFL TARD KAYKA VVNDA TIFK LELPLK QKG VGLKTQP ES KCPELLAN Y CDMLLRKTP LSKKLTSEEI EAKLKEVLL V LKYVQNKD VF MRYHKAH LTR RLILDI SADS EIEEN MVEWL REVG MPADYV NKL ARMFQDI KV SEDLNQAF K EMHKNNKLA LPADSVNIKI LNAGAWSRS S EKVFVSLP TE LEDLIPE VEE FYKKNH SGRK LHWHH LMSNG IITF KNEVGQ YDL EVTTFQL AV LFAWNQRP R EKISFENLK LATELPDAEL RRTLWSLVA F PKLKRQVL LY EPQVNSP KDF TEGTLF SVNQ EFSLI KNAKV QKRG KINLIG RLQ LTTERMR EE ENEGIVQL R ILRTQEAII QIMKMRKKIS NAQLQTELV E ILKNMFLP QK KMIKEQI EWL IEHKYI RRDE SDINT FIYMA

UniProtKB: Cullin-5

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Macromolecule #6: RING-box protein 2

MacromoleculeName: RING-box protein 2 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADVEDGEET CALASHSGS S GSKSGGDK MF SLKKWNA VAM WSWDVE CDTC AICRV QVMDA CLRC QAENKQ EDC VVVWGEC NH SFHNCCMS L WVKQNNRCP LCQQDWVVQR IGK

UniProtKB: RING-box protein 2

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Macromolecule #7: DNA dC->dU-editing enzyme APOBEC-3H

MacromoleculeName: DNA dC->dU-editing enzyme APOBEC-3H / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO / EC number: single-stranded DNA cytosine deaminase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGGSGGMAL LTAETFR LQ FNNKRRLR R PYYPRKALL CYQLTPQNGS TPTRGYFEN K KKCHAEIC FI NEIKSMG LDE TQCYQV TCYL TWSPC SSCAW ELVD FIQAHD HLN LRIFASR LY YHWCKPQQ D GLRLLCGSQ VPVEVMGFPE FADCWENFV D ...String:
GPGGSGGMAL LTAETFR LQ FNNKRRLR R PYYPRKALL CYQLTPQNGS TPTRGYFEN K KKCHAEIC FI NEIKSMG LDE TQCYQV TCYL TWSPC SSCAW ELVD FIQAHD HLN LRIFASR LY YHWCKPQQ D GLRLLCGSQ VPVEVMGFPE FADCWENFV D HEKPLSFN PY KMLEELD KNS RAIKRR LDRI KS

UniProtKB: DNA dC->dU-editing enzyme APOBEC-3H

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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
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 12546 / Average exposure time: 8.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 150000

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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.
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 5.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 98939
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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