[English] 日本語
Yorodumi
- PDB-7upn: Maedi visna virus Vif in complex with CypA and E3 ubiquitin ligase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7upn
TitleMaedi visna virus Vif in complex with CypA and E3 ubiquitin ligase
Components
  • Elongin-B
  • Elongin-C
  • Peptidyl-prolyl cis-trans isomerase A
  • Virion infectivity factor
KeywordsISOMERASE/VIRAL PROTEIN / 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 / VCB complex / regulation of viral genome replication ...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 / VCB complex / regulation of viral genome replication / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / virion binding / Basigin interactions / Cul5-RING ubiquitin ligase complex / 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 / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Calcineurin activates NFAT / viral release from host cell / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Binding and entry of HIV virion / positive regulation of viral genome replication / Formation of HIV elongation complex in the absence of HIV Tat / protein peptidyl-prolyl isomerization / RNA Polymerase II Transcription Elongation / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Formation of RNA Pol II elongation complex / positive regulation of protein dephosphorylation / RNA Polymerase II Pre-transcription Events / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / activation of protein kinase B activity / neutrophil chemotaxis / transcription corepressor binding / negative regulation of protein phosphorylation / peptidylprolyl isomerase / virion component / peptidyl-prolyl cis-trans isomerase activity / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of protein secretion / TP53 Regulates Transcription of DNA Repair Genes / Vif-mediated degradation of APOBEC3G / negative regulation of protein kinase activity / 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 aggregation / platelet activation / Regulation of expression of SLITs and ROBOs / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / integrin binding / protein folding / Platelet degranulation / cellular response to oxidative stress / Neddylation / positive regulation of NF-kappaB transcription factor activity / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / secretory granule lumen / vesicle / host cell cytoplasm / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / protein ubiquitination / positive regulation of protein phosphorylation / 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 / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Bovine Lentivirus VIF / Bovine Lentivirus VIF protein / Elongin B / Elongin-C / 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 B / Elongin-C / 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-like domain / Ubiquitin domain profile. / 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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHu, Y. / Xiong, Y.
Funding support United States, 1items
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, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase A
C: Virion infectivity factor
E: Elongin-C
H: Elongin-B
B: Peptidyl-prolyl cis-trans isomerase A
F: Virion infectivity factor
G: Elongin-C
I: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,55110
Polymers140,4218
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A


Mass: 18036.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase
#2: Protein Virion infectivity factor / Q protein


Mass: 28182.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Visna-maedi virus / Strain: KV1772 / Gene: vif / Production host: Escherichia coli (E. coli) / References: UniProt: P69717
#3: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10843.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#4: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 13147.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Maedi visna virus Vif in complex with human CypA and Elongin BC components of E3 ubiquitin ligase
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-2/1
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 62 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74320 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029084
ELECTRON MICROSCOPYf_angle_d0.48812256
ELECTRON MICROSCOPYf_dihedral_angle_d3.7161174
ELECTRON MICROSCOPYf_chiral_restr0.041284
ELECTRON MICROSCOPYf_plane_restr0.0051556

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more