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Yorodumi- EMDB-26673: Maedi visna virus Vif in complex with CypA and E3 ubiquitin ligase -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26673 | |||||||||
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Title | Maedi visna virus Vif in complex with CypA and E3 ubiquitin ligase | |||||||||
Map data | ||||||||||
Sample |
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Keywords | virus-host interacting complex / ISOMERASE-VIRAL PROTEIN complex | |||||||||
Function / homology | Function and homology information negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / target-directed miRNA degradation / heparan sulfate binding / elongin complex / regulation of viral genome replication / VCB complex ...negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / target-directed miRNA degradation / heparan sulfate binding / elongin complex / regulation of viral genome replication / VCB complex / virion binding / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / Cul5-RING ubiquitin ligase complex / Basigin interactions / 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 / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / viral release from host cell / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Calcineurin activates NFAT / protein peptidyl-prolyl isomerization / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Binding and entry of HIV virion / Formation of HIV elongation complex in the absence of HIV Tat / positive regulation of viral genome replication / RNA Polymerase II Transcription Elongation / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Formation of RNA Pol II elongation complex / : / RNA Polymerase II Pre-transcription Events / neutrophil chemotaxis / activation of protein kinase B activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / transcription corepressor binding / negative regulation of protein phosphorylation / platelet aggregation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / virion component / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / negative regulation of protein kinase activity / Vif-mediated degradation of APOBEC3G / Assembly Of The HIV Virion / Budding and maturation of HIV virion / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / neuron differentiation / platelet activation / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Platelet degranulation / protein folding / positive regulation of NF-kappaB transcription factor activity / Neddylation / protein-macromolecule adaptor activity / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / host cell cytoplasm / positive regulation of MAPK cascade / protein ubiquitination / positive regulation of protein phosphorylation / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / regulation of transcription by RNA polymerase II / apoptotic process / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Visna-maedi virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Hu Y / Xiong Y | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26673.map.gz | 21.5 MB | EMDB map data format | |
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Header (meta data) | emd-26673-v30.xml emd-26673.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
Images | emd_26673.png | 47.5 KB | ||
Filedesc metadata | emd-26673.cif.gz | 5.7 KB | ||
Others | emd_26673_half_map_1.map.gz emd_26673_half_map_2.map.gz | 39.7 MB 39.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26673 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26673 | HTTPS FTP |
-Validation report
Summary document | emd_26673_validation.pdf.gz | 815.6 KB | Display | EMDB validaton report |
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Full document | emd_26673_full_validation.pdf.gz | 815.1 KB | Display | |
Data in XML | emd_26673_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | emd_26673_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26673 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26673 | HTTPS FTP |
-Related structure data
Related structure data | 7upnMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26673.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_26673_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26673_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Maedi visna virus Vif in complex with human CypA and Elongin BC c...
Entire | Name: Maedi visna virus Vif in complex with human CypA and Elongin BC components of E3 ubiquitin ligase |
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Components |
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-Supramolecule #1: Maedi visna virus Vif in complex with human CypA and Elongin BC c...
Supramolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Peptidyl-prolyl cis-trans isomerase A
Macromolecule | Name: Peptidyl-prolyl cis-trans isomerase A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 18.036504 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: Virion infectivity factor
Macromolecule | Name: Virion infectivity factor / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Visna-maedi virus / Strain: KV1772 |
Molecular weight | Theoretical: 28.1826 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #3: Elongin-C
Macromolecule | Name: Elongin-C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.84342 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MYVKLISSDG HEFIVKREHA LTSGTIKAML SGPGQFAENE TNEVNFREIP SHVLSKVCMY FTYKVRYTNS STEIPEFPIA PEIALELLM AANFLDC UniProtKB: Elongin-C |
-Macromolecule #4: Elongin-B
Macromolecule | Name: Elongin-B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.147781 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ UniProtKB: Elongin-B |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Grid | Model: C-flat-2/1 / Material: COPPER / Support film - Material: GRAPHENE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Applied 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 assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |