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- EMDB-26673: Maedi visna virus Vif in complex with CypA and E3 ubiquitin ligase -

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Basic information

Entry
Database: EMDB / ID: EMD-26673
TitleMaedi visna virus Vif in complex with CypA and E3 ubiquitin ligase
Map data
Sample
  • Complex: Maedi visna virus Vif in complex with human CypA and Elongin BC components of E3 ubiquitin ligase
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase A
    • Protein or peptide: Virion infectivity factor
    • Protein or peptide: Elongin-C
    • Protein or peptide: Elongin-B
  • Ligand: ZINC ION
Keywordsvirus-host interacting complex / ISOMERASE-VIRAL PROTEIN complex
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / lipid droplet organization / target-directed miRNA degradation / VCB complex / heparan sulfate binding / elongin complex / regulation of viral genome replication ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / lipid droplet organization / target-directed miRNA degradation / VCB complex / heparan sulfate binding / elongin complex / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / Cul5-RING ubiquitin ligase complex / Basigin interactions / protein peptidyl-prolyl isomerization / Cul2-RING ubiquitin ligase complex / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of protein phosphorylation / Calcineurin activates NFAT / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Binding and entry of HIV virion / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / positive regulation of viral genome replication / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / neutrophil chemotaxis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / peptidyl-prolyl cis-trans isomerase activity / transcription corepressor binding / negative regulation of protein kinase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / positive regulation of protein secretion / peptidylprolyl isomerase / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Assembly Of The HIV Virion / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Budding and maturation of HIV virion / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / platelet activation / virion component / platelet aggregation / Regulation of expression of SLITs and ROBOs / neuron differentiation / positive regulation of NF-kappaB transcription factor activity / SARS-CoV-1 activates/modulates innate immune responses / integrin binding / unfolded protein binding / Antigen processing: Ubiquitination & Proteasome degradation / Platelet degranulation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding / positive regulation of protein phosphorylation / Neddylation / protein-containing complex assembly / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / host cell cytoplasm / positive regulation of MAPK cascade / protein ubiquitination / focal adhesion / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Bovine Lentivirus VIF / Bovine Lentivirus VIF protein / Elongin-C / Elongin B / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site ...Bovine Lentivirus VIF / Bovine Lentivirus VIF protein / Elongin-C / Elongin B / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / SKP1/BTB/POZ domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase A / Virion infectivity factor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human) / Visna-maedi virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHu Y / Xiong Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Sci Adv / Year: 2023
Title: Structural basis for recruitment of host CypA and E3 ubiquitin ligase by maedi-visna virus Vif.
Authors: Yingxia Hu / Ragna B Gudnadóttir / Kirsten M Knecht / Fidel Arizaga / Stefán R Jónsson / Yong Xiong /
Abstract: Lentiviral Vif molecules target the host antiviral APOBEC3 proteins for destruction in cellular ubiquitin-proteasome pathways. Different lentiviral Vifs have evolved to use the same canonical E3 ...Lentiviral Vif molecules target the host antiviral APOBEC3 proteins for destruction in cellular ubiquitin-proteasome pathways. Different lentiviral Vifs have evolved to use the same canonical E3 ubiquitin ligase complexes, along with distinct noncanonical host cofactors for their activities. Unlike primate lentiviral Vif, which recruits CBFβ as the noncanonical cofactor, nonprimate lentiviral Vif proteins have developed different cofactor recruitment mechanisms. Maedi-visna virus (MVV) sequesters CypA as the noncanonical cofactor for the Vif-mediated ubiquitination of ovine APOBEC3s. Here, we report the cryo-electron microscopy structure of MVV Vif in complex with CypA and E3 ligase components. The structure, along with our biochemical and functional analysis, reveals both conserved and unique structural elements of MVV Vif and its common and distinct interaction modes with various cognate cellular proteins, providing a further understanding of the evolutionary relationship between lentiviral Vifs and the molecular mechanisms by which they capture different host cofactors for immune evasion activities.
History
DepositionApr 16, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26673.png

Downloads & links

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Map

FileDownload / File: emd_26673.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 224 pix.
= 246.4 Å		1.1 Å/pix.
x 224 pix.
= 246.4 Å		1.1 Å/pix.
x 224 pix.
= 246.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.35306013 - 0.8071141
Average (Standard dev.)0.0030548964 (±0.026731413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 246.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_26673_half_map_1.map
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Half map: #1

Fileemd_26673_half_map_2.map
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Sample components

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Entire : Maedi visna virus Vif in complex with human CypA and Elongin BC c...

EntireName: Maedi visna virus Vif in complex with human CypA and Elongin BC components of E3 ubiquitin ligase
Components
  • Complex: Maedi visna virus Vif in complex with human CypA and Elongin BC components of E3 ubiquitin ligase
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase A
    • Protein or peptide: Virion infectivity factor
    • Protein or peptide: Elongin-C
    • Protein or peptide: Elongin-B
  • Ligand: ZINC ION

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Supramolecule #1: Maedi visna virus Vif in complex with human CypA and Elongin BC c...

SupramoleculeName: Maedi visna virus Vif in complex with human CypA and Elongin BC components of E3 ubiquitin ligase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Peptidyl-prolyl cis-trans isomerase A

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.036504 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVNPTVFFDI AVDGEPLGRV SFELFADKVP KTAENFRALS TGEKGFGYKG SCFHRIIPGF MCQGGDFTRH NGTGGKSIYG EKFEDENFI LKHTGPGILS MANAGPNTNG SQFFICTAKT EWLDGKHVVF GKVKEGMNIV EAMERFGSRN GKTSKKITIA D CGQLE

UniProtKB: Peptidyl-prolyl cis-trans isomerase A

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Macromolecule #2: Virion infectivity factor

MacromoleculeName: Virion infectivity factor / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Visna-maedi virus / Strain: KV1772
Molecular weightTheoretical: 28.1826 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLSSYRHQKK YKKNKAREIG PQLPLWAWKE TAFSINQEPY WYSTIRLQGL MWNKRGHKLM FVKENQGYEY WETSGKQWKM EIRRDLDLI AQINFRNAWQ YKSQGEWKTI GVWYESPGDY KGKENQFWFH WRIALCSCNK TRWDIREFMI GKHRWDLCKS C IQGEIVKN ...String:
MLSSYRHQKK YKKNKAREIG PQLPLWAWKE TAFSINQEPY WYSTIRLQGL MWNKRGHKLM FVKENQGYEY WETSGKQWKM EIRRDLDLI AQINFRNAWQ YKSQGEWKTI GVWYESPGDY KGKENQFWFH WRIALCSCNK TRWDIREFMI GKHRWDLCKS C IQGEIVKN TNPRSLQRLA LLHLAKDHVF QVMPLWRARR VTVQKFPWCR SPMGYTIPWS LQECWEMESI FE

UniProtKB: Virion infectivity factor

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Macromolecule #3: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.84342 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MYVKLISSDG HEFIVKREHA LTSGTIKAML SGPGQFAENE TNEVNFREIP SHVLSKVCMY FTYKVRYTNS STEIPEFPIA PEIALELLM AANFLDC

UniProtKB: Elongin-C

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Macromolecule #4: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.147781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ

UniProtKB: Elongin-B

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / 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
GridModel: C-flat-2/1 / Material: COPPER / Support film - Material: GRAPHENE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74320
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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