|Entry||Database: EMDB / ID: EMD-9631|
|Title||The structure of ICAM-5 triggered Enterovirus D68 virus A-particle|
virus / (Capsid protein ...Capsid) x 3
|Function / homology|
Function and homology information
picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / pore formation by virus in membrane of host cell ...picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / pore formation by virus in membrane of host cell / integral to membrane of host cell / nucleoside-triphosphate phosphatase / viral capsid / protein complex oligomerization / induction by virus of host autophagy / RNA-directed RNA polymerase / ion channel activity / suppression by virus of host gene expression / peptidase activity / viral RNA genome replication / RNA helicase activity / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / viral process / RNA binding / membrane / ATP binding
Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / Picornavirus 2B protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / Picornavirus coat protein VP4 / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / AAA+ ATPase domain ...Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / Picornavirus 2B protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / Picornavirus coat protein VP4 / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / AAA+ ATPase domain / Poliovirus 3A protein-like / P-loop containing nucleoside triphosphate hydrolase / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Poliovirus core protein 3a, soluble domain / Picornavirus coat protein VP4 superfamily / Peptidase C3, picornavirus core protein 2A
Genome polyprotein / Polyprotein
|Biological species||Enterovirus D / Enterovirus D68|
|Method||single particle reconstruction / cryo EM / Resolution: 4 Å|
|Authors||Zheng QB / Zhu R / Xu LF / He MZ / Yan XD / Cheng T / Li SW|
|Citation||Journal: Nat Microbiol / Year: 2019|
Title: Atomic structures of enterovirus D68 in complex with two monoclonal antibodies define distinct mechanisms of viral neutralization.
Authors: Qingbing Zheng / Rui Zhu / Longfa Xu / Maozhou He / Xiaodong Yan / Dongxiao Liu / Zhichao Yin / Yangtao Wu / Yongchao Li / Lisheng Yang / Wangheng Hou / Shuxuan Li / Zizhen Li / Zhenqin Chen / Zhihai Li / Hai Yu / Ying Gu / Jun Zhang / Timothy S Baker / Z Hong Zhou / Barney S Graham / Tong Cheng / Shaowei Li / Ningshao Xia /
Abstract: Enterovirus D68 (EV-D68) undergoes structural transformation between mature, cell-entry intermediate (A-particle) and empty forms throughout its life cycle. Structural information for the various ...Enterovirus D68 (EV-D68) undergoes structural transformation between mature, cell-entry intermediate (A-particle) and empty forms throughout its life cycle. Structural information for the various forms and antibody-bound capsids will facilitate the development of effective vaccines and therapeutics against EV-D68 infection, which causes childhood respiratory and paralytic diseases worldwide. Here, we report the structures of three EV-D68 capsid states representing the virus at major phases. We further describe two original monoclonal antibodies (15C5 and 11G1) with distinct structurally defined mechanisms for virus neutralization. 15C5 and 11G1 engage the capsid loci at icosahedral three-fold and five-fold axes, respectively. To block viral attachment, 15C5 binds three forms of capsids, and triggers mature virions to transform into A-particles, mimicking engagement by the functional receptor ICAM-5, whereas 11G1 exclusively recognizes the A-particle. Our data provide a structural and molecular explanation for the transition of picornavirus capsid conformations and demonstrate distinct mechanisms for antibody-mediated neutralization.
|Validation Report||PDB-ID: 6aj2|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_9631.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.128 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Enterovirus D
|Entire||Name: Enterovirus D / Number of components: 4|
-Component #1: virus, Enterovirus D
|Virus||Name: Enterovirus D / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN|
|Species||Species: Enterovirus D|
-Component #2: protein, Capsid protein VP1
|Protein||Name: Capsid protein VP1 / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 32.673035 kDa|
|Source||Species: Enterovirus D68|
-Component #3: protein, Capsid protein VP2
|Protein||Name: Capsid protein VP2 / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 27.567135 kDa|
|Source||Species: Enterovirus D68|
-Component #4: protein, Capsid protein VP3
|Protein||Name: Capsid protein VP3 / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 27.142842 kDa|
|Source||Species: Enterovirus D68|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7.4|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F30|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 9625|
|3D reconstruction||Software: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution estimation)|
-Atomic model buiding
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