+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10222 | |||||||||
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Title | Cryo-EM structure of rhinovirus-A89 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information : / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C ...: / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / viral capsid / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / host cell cytoplasm / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding / membrane / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | HRV-89 (virus) / Rhinovirus A | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Wald J / Goessweiner-Mohr N / Blaas D / Pasin M | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Cryo-EM structure of pleconaril-resistant rhinovirus-B5 complexed to the antiviral OBR-5-340 reveals unexpected binding site. Authors: Jiri Wald / Marion Pasin / Martina Richter / Christin Walther / Neann Mathai / Johannes Kirchmair / Vadim A Makarov / Nikolaus Goessweiner-Mohr / Thomas C Marlovits / Irene Zanella / Antonio ...Authors: Jiri Wald / Marion Pasin / Martina Richter / Christin Walther / Neann Mathai / Johannes Kirchmair / Vadim A Makarov / Nikolaus Goessweiner-Mohr / Thomas C Marlovits / Irene Zanella / Antonio Real-Hohn / Nuria Verdaguer / Dieter Blaas / Michaela Schmidtke / Abstract: Viral inhibitors, such as pleconaril and vapendavir, target conserved regions in the capsids of rhinoviruses (RVs) and enteroviruses (EVs) by binding to a hydrophobic pocket in viral capsid protein 1 ...Viral inhibitors, such as pleconaril and vapendavir, target conserved regions in the capsids of rhinoviruses (RVs) and enteroviruses (EVs) by binding to a hydrophobic pocket in viral capsid protein 1 (VP1). In resistant RVs and EVs, bulky residues in this pocket prevent their binding. However, recently developed pyrazolopyrimidines inhibit pleconaril-resistant RVs and EVs, and computational modeling has suggested that they also bind to the hydrophobic pocket in VP1. We studied the mechanism of inhibition of pleconaril-resistant RVs using RV-B5 (1 of the 7 naturally pleconaril-resistant rhinoviruses) and OBR-5-340, a bioavailable pyrazolopyrimidine with proven in vivo activity, and determined the 3D-structure of the protein-ligand complex to 3.6 Å with cryoelectron microscopy. Our data indicate that, similar to other capsid binders, OBR-5-340 induces thermostability and inhibits viral adsorption and uncoating. However, we found that OBR-5-340 attaches closer to the entrance of the pocket than most other capsid binders, whose viral complexes have been studied so far, showing only marginal overlaps of the attachment sites. Comparing the experimentally determined 3D structure with the control, RV-B5 incubated with solvent only and determined to 3.2 Å, revealed no gross conformational changes upon OBR-5-340 binding. The pocket of the naturally OBR-5-340-resistant RV-A89 likewise incubated with OBR-5-340 and solved to 2.9 Å was empty. Pyrazolopyrimidines have a rigid molecular scaffold and may thus be less affected by a loss of entropy upon binding. They interact with less-conserved regions than known capsid binders. Overall, pyrazolopyrimidines could be more suitable for the development of new, broadly active inhibitors. | |||||||||
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_10222.map.gz | 73.7 MB | EMDB map data format | |
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Header (meta data) | emd-10222-v30.xml emd-10222.xml | 19 KB 19 KB | Display Display | EMDB header |
Images | emd_10222.png | 328.4 KB | ||
Masks | emd_10222_msk_1.map | 347.6 MB | Mask map | |
Others | emd_10222_half_map_1.map.gz emd_10222_half_map_2.map.gz | 275.8 MB 275.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10222 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10222 | HTTPS FTP |
-Related structure data
Related structure data | 6sk7MC 6sk5C 6sk6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10222.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.97 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10222_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10222_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10222_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rhinovirus A
Entire | Name: Rhinovirus A |
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Components |
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-Supramolecule #1: Rhinovirus A
Supramolecule | Name: Rhinovirus A / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 650130 / Sci species name: Rhinovirus A / Sci species strain: A89 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
Virus shell | Shell ID: 1 / Name: VP1-4 / Diameter: 302.0 Å |
-Macromolecule #1: VP1 capsid protein
Macromolecule | Name: VP1 capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: HRV-89 (virus) |
Molecular weight | Theoretical: 33.288102 KDa |
Sequence | String: NPVENYIDSV LNEVLVVPNI QPSTSVSSHA APALDAAETG HTSSVQPEDM IETRYVITDQ TRDETSIESF LGRSGCIAMI EFNTSSDKT EHDKIGKGFK TWKVSLQEMA QIRRKYELFT YTRFDSEITI VTAAAAQGND SGHIVLQFMY VPPGAPVPEK R DDYTWQSG ...String: NPVENYIDSV LNEVLVVPNI QPSTSVSSHA APALDAAETG HTSSVQPEDM IETRYVITDQ TRDETSIESF LGRSGCIAMI EFNTSSDKT EHDKIGKGFK TWKVSLQEMA QIRRKYELFT YTRFDSEITI VTAAAAQGND SGHIVLQFMY VPPGAPVPEK R DDYTWQSG TNASVFWQEG QPYPRFTIPF MSIASAYYMF YDGYDGDSAA SKYGSVVTND MGTICVRIVT SNQKHDSNIV CR IYHKAKH IKAWCPRPPR AVAYQHTHST NYIPSNGEAT TQIKTRPDVF TVTNVGPSSM F |
-Macromolecule #2: VP2 capsid protein
Macromolecule | Name: VP2 capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: HRV-89 (virus) |
Molecular weight | Theoretical: 29.422793 KDa |
Sequence | String: SPTVEACGYS DRLIQITRGD STITSQDTAN AVVAYGVWPS YLTPDDATAI DKPTQPDTSS NRFYTLDSRS WTSASSGWWW KLPDALKNM GIFGENMFYH FLGRSGYTIH VQCNSSKFHQ GLLIVAAIPE HQLASATSGN VSVGYNHTHP GEQGREVVPS R TSSDNKRP ...String: SPTVEACGYS DRLIQITRGD STITSQDTAN AVVAYGVWPS YLTPDDATAI DKPTQPDTSS NRFYTLDSRS WTSASSGWWW KLPDALKNM GIFGENMFYH FLGRSGYTIH VQCNSSKFHQ GLLIVAAIPE HQLASATSGN VSVGYNHTHP GEQGREVVPS R TSSDNKRP SDDSWLNFDG TLLGNLPIYP HQYINLRTNN SATLILPYVN AVPMDSMLRH NNWSLVIIPI CPLQVQPGGT QS IPITVSI SPMFSEFSGP RSKVVFSTTQ |
-Macromolecule #3: VP3 capsid protein
Macromolecule | Name: VP3 capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: HRV-89 (virus) |
Molecular weight | Theoretical: 26.325994 KDa |
Sequence | String: GLPVMLTPGS GQFLTTDDTQ SPSAFPYFHP TKEIFIPGQV RNLIEMCQVD TLIPVNNTQE NVRSVNMYTV DLRTQVDLAK EVFSIPVDI ASQPLATTLI GELASYYTHW TGSLRFSFMF CGSASSTLKL LIAYTPPGVG KPKSRREAML GTHLVWDVGL Q STASLVVP ...String: GLPVMLTPGS GQFLTTDDTQ SPSAFPYFHP TKEIFIPGQV RNLIEMCQVD TLIPVNNTQE NVRSVNMYTV DLRTQVDLAK EVFSIPVDI ASQPLATTLI GELASYYTHW TGSLRFSFMF CGSASSTLKL LIAYTPPGVG KPKSRREAML GTHLVWDVGL Q STASLVVP WVSASHFRFT TPDTYSSAGY ITCWYQTNFV VPDSTPDNAK MVCMVSACKD FCLRLARDTN LHTQEGVLTQ |
-Macromolecule #4: VP4 capsid protein
Macromolecule | Name: VP4 capsid protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: HRV-89 (virus) |
Molecular weight | Theoretical: 7.461104 KDa |
Sequence | String: MGAQVSRQNV GTHSTQNSVS NGSSLNYFNI NYFKDAASSG ASRLDFSQDP SKFTDPVKDV LEKGIPTLQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Component:
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Grid | Model: Homemade / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.4 nm / Pretreatment - Type: GLOW DISCHARGE | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-25 / Number real images: 5370 / Average exposure time: 5.0 sec. / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 4.1) |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C60 (60 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107054 |