+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32194 | |||||||||
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Title | Coxsackievirus B3 (VP3-234Q) incubation with CD55 at pH7.4 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information : / symbiont-mediated perturbation of host gene expression / negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) ...: / symbiont-mediated perturbation of host gene expression / negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / COPI-mediated anterograde transport / side of membrane / complement activation, classical pathway / transport vesicle / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / endoplasmic reticulum-Golgi intermediate compartment membrane / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / secretory granule membrane / T=pseudo3 icosahedral viral capsid / Regulation of Complement cascade / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / positive regulation of T cell cytokine production / : / nucleoside-triphosphate phosphatase / virus receptor activity / protein complex oligomerization / monoatomic ion channel activity / positive regulation of cytosolic calcium ion concentration / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / membrane raft / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / Golgi membrane / RNA-dependent RNA polymerase activity / innate immune response / DNA-templated transcription / lipid binding / host cell nucleus / Neutrophil degranulation / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Coxsackievirus B3 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||
Authors | Wang QL / Liu CC | |||||||||
Funding support | China, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: Molecular basis of differential receptor usage for naturally occurring CD55-binding and -nonbinding coxsackievirus B3 strains. Authors: Qingling Wang / Qian Yang / Congcong Liu / Guoqing Wang / Hao Song / Guijun Shang / Ruchao Peng / Xiao Qu / Sheng Liu / Yingzi Cui / Peiyi Wang / Wenbo Xu / Xin Zhao / Jianxun Qi / Mengsu Yang / George F Gao / Abstract: Receptor usage defines cell tropism and contributes to cell entry and infection. Coxsackievirus B (CVB) engages coxsackievirus and adenovirus receptor (CAR), and selectively utilizes the decay- ...Receptor usage defines cell tropism and contributes to cell entry and infection. Coxsackievirus B (CVB) engages coxsackievirus and adenovirus receptor (CAR), and selectively utilizes the decay-accelerating factor (DAF; CD55) to infect cells. However, the differential receptor usage mechanism for CVB remains elusive. This study identified VP3-234 residues (234Q/N/V/D/E) as critical population selection determinants during CVB3 virus evolution, contributing to diverse binding affinities to CD55. Cryoelectron microscopy (cryo-EM) structures of CD55-binding/nonbinding isolates and their complexes with CD55 or CAR were obtained under both neutral and acidic conditions, and the molecular mechanism of VP3-234 residues determining CD55 affinity/specificity for naturally occurring CVB3 strains was elucidated. Structural and biochemical studies in vitro revealed the dynamic entry process of CVB3 and the function of the uncoating receptor CAR with different pH preferences. This work provides detailed insight into the molecular mechanism of CVB infection and contributes to an in-depth understanding of enterovirus attachment receptor usage. | |||||||||
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_32194.map.gz | 84.7 MB | EMDB map data format | |
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Header (meta data) | emd-32194-v30.xml emd-32194.xml | 20.4 KB 20.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32194_fsc.xml | 15.3 KB | Display | FSC data file |
Images | emd_32194.png | 121.6 KB | ||
Masks | emd_32194_msk_1.map | 307.5 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32194 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32194 | HTTPS FTP |
-Related structure data
Related structure data | 7vy5MC 7vxhC 7vxzC 7vy0C 7vy6C 7vykC 7vylC 7vymC 7w14C 7w17C 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_32194.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 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_32194_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Coxsackievirus B3
Entire | Name: Coxsackievirus B3 |
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Components |
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-Supramolecule #1: Coxsackievirus B3
Supramolecule | Name: Coxsackievirus B3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / NCBI-ID: 12072 / Sci species name: Coxsackievirus B3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
Host system | Organism: Homo sapiens (human) |
-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Coxsackievirus B3 |
Molecular weight | Theoretical: 30.167762 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: RVADTVGTGP TNSEAIPALT AAETGHTSQV VPGDTMQTRH VKNYHSRSES TIENFLCRSA CVYFTEYENS GAKRYAEWVL TPRQAAQLR RKLEFFTYVR FDLELTFVIT STQQPSTTQN QDAQILTHQI MYVPPGGPVP DKVDSYVWQT STNPSVFWTE G NAPPRMSI ...String: RVADTVGTGP TNSEAIPALT AAETGHTSQV VPGDTMQTRH VKNYHSRSES TIENFLCRSA CVYFTEYENS GAKRYAEWVL TPRQAAQLR RKLEFFTYVR FDLELTFVIT STQQPSTTQN QDAQILTHQI MYVPPGGPVP DKVDSYVWQT STNPSVFWTE G NAPPRMSI PFLSIGNAYS NFYDGWSEFS RNGVYGINTL NNMGTLYARH VNAGSTGPIK STIRIYFKPK HVKAWIPRPP RL CQYEKAK NVNFQPSGVT TTRQSITTMT N |
-Macromolecule #2: Capsid protein VP2
Macromolecule | Name: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Coxsackievirus B3 |
Molecular weight | Theoretical: 28.076682 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GYSDRARSIT LGNSTITTQE CANVVVGYGV WPDYLKDSEA TAEDQPTQPD VATCRFYTLD SVQWQKTSPG WWWKLPDALS NLGLFGQNM QYHYLGRTGY TVHVQCNASK FHQGCLLVVC VPEAEMGCAT LDNTPSSAEL LGGDSAKEFA DKPVASGSNK L VQRVVYNA ...String: GYSDRARSIT LGNSTITTQE CANVVVGYGV WPDYLKDSEA TAEDQPTQPD VATCRFYTLD SVQWQKTSPG WWWKLPDALS NLGLFGQNM QYHYLGRTGY TVHVQCNASK FHQGCLLVVC VPEAEMGCAT LDNTPSSAEL LGGDSAKEFA DKPVASGSNK L VQRVVYNA GMGVGVGNLT IFPHQWINLR TNNSATIVMP YTNSVPMDNM FRHNNVTLMV IPFVPLDYCP GSTTYVPITV TI APMCAEY NGLRLAGHQ |
-Macromolecule #3: Capsid protein VP3
Macromolecule | Name: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Coxsackievirus B3 |
Molecular weight | Theoretical: 26.227725 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GLPTMNTPGS CQFLTSDDFQ SPSAMPQYDV TPEMRIPGEV KNLMEIAEVD SVVPVQNVGE KVNSMEAYQI PVRSNEGSGT QVFGFPLQP GYSSVFSRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GAPTKRVDAM LGTHVVWDVG L QSSCVLCI ...String: GLPTMNTPGS CQFLTSDDFQ SPSAMPQYDV TPEMRIPGEV KNLMEIAEVD SVVPVQNVGE KVNSMEAYQI PVRSNEGSGT QVFGFPLQP GYSSVFSRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GAPTKRVDAM LGTHVVWDVG L QSSCVLCI PWISQTHYRY VTSDEYTAGG FITCWYQTNI VVPADAQSSC YIMCFVSACN DFSVRLLKDT PFISQQNFFQ |
-Macromolecule #4: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Coxsackievirus B3 / Strain: Nancy |
Molecular weight | Theoretical: 7.349039 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GAQVSTQKTG AHETGLNASG NSIIHYTNIN YYKDAASNSA NRQDFTQDPG KFTEPVKDIM IKSLPALN |
-Macromolecule #5: Complement decay-accelerating factor
Macromolecule | Name: Complement decay-accelerating factor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.535401 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: CEVPTRLNSA SLKQPYITQN YFPVGTVVEY ECRPGYRREP SLSPKLTCLQ NLKWSTAVEF CKKKSCPNPG EIRNGQIDVP GGILFGATI SFSCNTGYKL FGSTSSFCLI SGSSVQWSDP LPEC |
-Macromolecule #6: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ChemComp-PLM: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 1.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 70.0 K / Max: 70.0 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |