+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4060 | |||||||||
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Title | Negative Stain electron microscopy of GIF:IL2 complex | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Ovis aries (sheep) / Orf virus | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 17.0 Å | |||||||||
Authors | Kandiah E / Gutsche I | |||||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF. Authors: Jan Felix / Eaazhisai Kandiah / Steven De Munck / Yehudi Bloch / Gydo C P van Zundert / Kris Pauwels / Ann Dansercoer / Katka Novanska / Randy J Read / Alexandre M J J Bonvin / Bjorn ...Authors: Jan Felix / Eaazhisai Kandiah / Steven De Munck / Yehudi Bloch / Gydo C P van Zundert / Kris Pauwels / Ann Dansercoer / Katka Novanska / Randy J Read / Alexandre M J J Bonvin / Bjorn Vergauwen / Kenneth Verstraete / Irina Gutsche / Savvas N Savvides / Abstract: Subversion of the host immune system by viruses is often mediated by molecular decoys that sequester host proteins pivotal to mounting effective immune responses. The widespread mammalian pathogen ...Subversion of the host immune system by viruses is often mediated by molecular decoys that sequester host proteins pivotal to mounting effective immune responses. The widespread mammalian pathogen parapox Orf virus deploys GIF, a member of the poxvirus immune evasion superfamily, to antagonize GM-CSF (granulocyte macrophage colony-stimulating factor) and IL-2 (interleukin-2), two pleiotropic cytokines of the mammalian immune system. However, structural and mechanistic insights into the unprecedented functional duality of GIF have remained elusive. Here we reveal that GIF employs a dimeric binding platform that sequesters two copies of its target cytokines with high affinity and slow dissociation kinetics to yield distinct complexes featuring mutually exclusive interaction footprints. We illustrate how GIF serves as a competitive decoy receptor by leveraging binding hotspots underlying the cognate receptor interactions of GM-CSF and IL-2, without sharing any structural similarity with the cytokine receptors. Our findings contribute to the tracing of novel molecular mimicry mechanisms employed by pathogenic viruses. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4060.map.gz | 456.6 KB | EMDB map data format | |
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Header (meta data) | emd-4060-v30.xml emd-4060.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_4060.png | 72.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4060 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4060 | HTTPS FTP |
-Validation report
Summary document | emd_4060_validation.pdf.gz | 198.2 KB | Display | EMDB validaton report |
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Full document | emd_4060_full_validation.pdf.gz | 197.3 KB | Display | |
Data in XML | emd_4060_validation.xml.gz | 4.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4060 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4060 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4060.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 3.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex of GIF:IL2
Entire | Name: Complex of GIF:IL2 |
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Components |
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-Supramolecule #1: Complex of GIF:IL2
Supramolecule | Name: Complex of GIF:IL2 / type: complex / ID: 1 / Parent: 0 Details: Ovine cytokine Interleukin-2 is complexed with orf virus decoy receptor GIF. |
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Source (natural) | Organism: Ovis aries (sheep) |
-Supramolecule #2: Ovine cytokine Interleukin-2
Supramolecule | Name: Ovine cytokine Interleukin-2 / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Ovis aries (sheep) |
Recombinant expression | Organism: HEK293T (human) / Recombinant plasmid: pHLsec |
-Supramolecule #3: Orf virus decoy receptor GIF.
Supramolecule | Name: Orf virus decoy receptor GIF. / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Orf virus |
Recombinant expression | Organism: HEK293T (human) / Recombinant plasmid: pHLsec |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Staining | Type: NEGATIVE / Material: Uranyl acetate Details: Negatively stained EM specimens were prepared using a carbon-sandwich technique and 2% (w/v) uranyl-acetate stain. |
-Electron microscopy
Microscope | JEOL 1200EXII |
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Image recording | Film or detector model: KODAK SO-163 FILM / Average electron dose: 10.0 e/Å2 |
Electron beam | Acceleration voltage: 100 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 40000 |
-Image processing
Startup model | Type of model: INSILICO MODEL / In silico model: Ab-inition 3D reconstruction using VIPER |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 24324 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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