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Yorodumi- EMDB-32189: Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32189 | |||||||||
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Title | Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 20min | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host transcription / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / germ cell migration ...AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host transcription / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / germ cell migration / apicolateral plasma membrane / transepithelial transport / cell-cell junction organization / connexin binding / cardiac muscle cell development / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / intercalated disc / bicellular tight junction / cell adhesion molecule binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / neutrophil chemotaxis / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / acrosomal vesicle / mitochondrion organization / T=pseudo3 icosahedral viral capsid / filopodium / PDZ domain binding / Cell surface interactions at the vascular wall / adherens junction / host cell cytoplasmic vesicle membrane / neuromuscular junction / endocytosis involved in viral entry into host cell / beta-catenin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / integrin binding / nucleoside-triphosphate phosphatase / cell junction / protein complex oligomerization / monoatomic ion channel activity / virus receptor activity / heart development / cell body / growth cone / actin cytoskeleton organization / basolateral plasma membrane / defense response to virus / DNA replication / RNA helicase activity / neuron projection / induction by virus of host autophagy / membrane raft / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / signaling receptor binding / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / protein-containing complex / proteolysis / RNA binding / extracellular space / extracellular region / nucleoplasm / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Coxsackievirus B3 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.19 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_32189.map.gz | 95.5 MB | EMDB map data format | |
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Header (meta data) | emd-32189-v30.xml emd-32189.xml | 22.1 KB 22.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32189_fsc.xml | 15.3 KB | Display | FSC data file |
Images | emd_32189.png | 105 KB | ||
Masks | emd_32189_msk_1.map | 307.5 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32189 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32189 | HTTPS FTP |
-Related structure data
Related structure data | 7vxzMC 7vxhC 7vy0C 7vy5C 7vy6C 7vykC 7vylC 7vymC 7w14C 7w17C C: citing same article (ref.) M: atomic model generated by this map |
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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_32189.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_32189_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Coxsackievirus B3 with adenovirus receptor
Entire | Name: Coxsackievirus B3 with adenovirus receptor |
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Components |
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-Supramolecule #1: Coxsackievirus B3 with adenovirus receptor
Supramolecule | Name: Coxsackievirus B3 with adenovirus receptor / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #3: adenovirus receptor
Supramolecule | Name: adenovirus receptor / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #5 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #2: Coxsackievirus B3
Supramolecule | Name: Coxsackievirus B3 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 / 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: 31.639371 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GPVEDAITAA IGRVADTVGT GPTNSEAIPA LTAAETGHTS QVVPGDTMQT RHVKNYHSRS ESTIENFLCR SACVYFTEYE NSGAKRYAE WVLTPRQAAQ LRRKLEFFTY VRFDLELTFV ITSTQQPSTT QNQDAQILTH QIMYVPPGGP VPDKVDSYVW Q TSTNPSVF ...String: GPVEDAITAA IGRVADTVGT GPTNSEAIPA LTAAETGHTS QVVPGDTMQT RHVKNYHSRS ESTIENFLCR SACVYFTEYE NSGAKRYAE WVLTPRQAAQ LRRKLEFFTY VRFDLELTFV ITSTQQPSTT QNQDAQILTH QIMYVPPGGP VPDKVDSYVW Q TSTNPSVF WTEGNAPPRM SIPFLSIGNA YSNFYDGWSE FSRNGVYGIN TLNNMGTLYA RHVNAGSTGP IKSTIRIYFK PK HVKAWIP RPPRLCQYEK AKNVNFQPSG VTTTRQSITT MTNTGAF |
-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: 28.822475 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SPTVEECGYS DRARSITLGN STITTQECAN VVVGYGVWPD YLKDSEATAE DQPTQPDVAT CRFYTLDSVQ WQKTSPGWWW KLPDALSNL GLFGQNMQYH YLGRTGYTVH VQCNASKFHQ GCLLVVCVPE AEMGCATLDN TPSSAELLGG DSAKEFADKP V ASGSNKLV ...String: SPTVEECGYS DRARSITLGN STITTQECAN VVVGYGVWPD YLKDSEATAE DQPTQPDVAT CRFYTLDSVQ WQKTSPGWWW KLPDALSNL GLFGQNMQYH YLGRTGYTVH VQCNASKFHQ GCLLVVCVPE AEMGCATLDN TPSSAELLGG DSAKEFADKP V ASGSNKLV QRVVYNAGMG VGVGNLTIFP HQWINLRTNN SATIVMPYTN SVPMDNMFRH NNVTLMVIPF VPLDYCPGST TY VPITVTI APMCAEYNGL RLAGHQ |
-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: Capsid protein VP4
Macromolecule | Name: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Coxsackievirus B3 |
Molecular weight | Theoretical: 7.480235 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGAQVSTQKT GAHETGLNAS GNSIIHYTNI NYYKDAASNS ANRQDFTQDP GKFTEPVKDI MIKSLPALN |
-Macromolecule #5: Coxsackievirus and adenovirus receptor
Macromolecule | Name: Coxsackievirus and adenovirus receptor / 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: 25.106408 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSITTPEEMI EKAKGETAYL PCKFTLSPED QGPLDIEWLI SPADNQKVDQ VIILYSGDKI YDDYYPDLKG RVHFTSNDLK SGDASINVT NLQLSDIGTY QCKVKKAPGV ANKKIHLVVL VKPSGARCYV DGSEEIGSDF KIKCEPKEGS LPLQYEWQKL S DSQKMPTS ...String: MSITTPEEMI EKAKGETAYL PCKFTLSPED QGPLDIEWLI SPADNQKVDQ VIILYSGDKI YDDYYPDLKG RVHFTSNDLK SGDASINVT NLQLSDIGTY QCKVKKAPGV ANKKIHLVVL VKPSGARCYV DGSEEIGSDF KIKCEPKEGS LPLQYEWQKL S DSQKMPTS WLAEMTSSVI SVKNASSEYS GTYSCTVRNR VGSDQCLLRL NVVPPSNKAL EHHHHHH |
-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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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 |
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 FIELD / 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |