[English] 日本語
Yorodumi- EMDB-2761: Structural Basis of Human Parechovirus Neutralization by Human Mo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2761 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structural Basis of Human Parechovirus Neutralization by Human Monoclonal Antibodies | |||||||||
Map data | Reconstruction of human parechovirus 1 in complex with Fab fragments of AM28 human monoclonal antibody | |||||||||
Sample |
| |||||||||
Keywords | Human parechovirus 1 / AM28 / human monoclonal antibody / HPeV1-AM28 Fab | |||||||||
Function / homology | Function and homology information host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / nucleoside-triphosphate phosphatase / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / nucleoside-triphosphate phosphatase / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human parechovirus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 19.76 Å | |||||||||
Authors | Shakeel S / Westerhuis BM / Ora A / Koen G / Bakker A / Claassen Y / Beaumont T / Wolthers K / Butcher SJ | |||||||||
Citation | Journal: J Virol / Year: 2015 Title: Structural Basis of Human Parechovirus Neutralization by Human Monoclonal Antibodies. Authors: Shabih Shakeel / Brenda M Westerhuis / Ari Ora / Gerrit Koen / Arjen Q Bakker / Yvonne Claassen / Koen Wagner / Tim Beaumont / Katja C Wolthers / Sarah J Butcher / Abstract: Since it was first recognized in 2004 that human parechoviruses (HPeV) are a significant cause of central nervous system and neonatal sepsis, their clinical importance, primarily in children, has ...Since it was first recognized in 2004 that human parechoviruses (HPeV) are a significant cause of central nervous system and neonatal sepsis, their clinical importance, primarily in children, has started to emerge. Intravenous immunoglobulin treatment is the only treatment available in such life-threatening cases and has given moderate success. Direct inhibition of parechovirus infection using monoclonal antibodies is a potential treatment. We have developed two neutralizing monoclonal antibodies against HPeV1 and HPeV2, namely, AM18 and AM28, which also cross-neutralize other viruses. Here, we present the mapping of their epitopes using peptide scanning, surface plasmon resonance, fluorescence-based thermal shift assays, electron cryomicroscopy, and image reconstruction. We determined by peptide scanning and surface plasmon resonance that AM18 recognizes a linear epitope motif including the arginine-glycine-aspartic acid on the C terminus of capsid protein VP1. This epitope is normally used by the virus to attach to host cell surface integrins during entry and is found in 3 other viruses that AM18 neutralizes. Therefore, AM18 is likely to cause virus neutralization by aggregation and by blocking integrin binding to the capsid. Further, we show by electron cryomicroscopy, three-dimensional reconstruction, and pseudoatomic model fitting that ordered RNA interacts with HPeV1 VP1 and VP3. AM28 recognizes quaternary epitopes on the capsid composed of VP0 and VP3 loops from neighboring pentamers, thereby increasing the RNA accessibility temperature for the virus-AM28 complex compared to the virus alone. Thus, inhibition of RNA uncoating probably contributes to neutralization by AM28. IMPORTANCE: Human parechoviruses can cause mild infections to severe diseases in young children, such as neonatal sepsis, encephalitis, and cardiomyopathy. Intravenous immunoglobulin treatment is the ...IMPORTANCE: Human parechoviruses can cause mild infections to severe diseases in young children, such as neonatal sepsis, encephalitis, and cardiomyopathy. Intravenous immunoglobulin treatment is the only treatment available in such life-threatening cases. In order to develop more targeted treatment, we have searched for human monoclonal antibodies that would neutralize human parechoviruses 1 and 2, associated with mild infections such as gastroenteritis and severe infections of the central nervous system, and thus allow safe treatment. In the current study, we show how two such promising antibodies interact with the virus, modeling the atomic interactions between the virus and the antibody to propose how neutralization occurs. Both antibodies can cause aggregation; in addition, one antibody interferes with the virus recognizing its target cell, while the other, recognizing only the whole virus, inhibits the genome uncoating and replication in the cell. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2761.map.gz | 7.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-2761-v30.xml emd-2761.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_2761_fsc.xml | 3.7 KB | Display | FSC data file |
Images | EMD-2761.jpg emd_2761.jpg | 37.4 KB 37.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2761 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2761 | HTTPS FTP |
-Validation report
Summary document | emd_2761_validation.pdf.gz | 236.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_2761_full_validation.pdf.gz | 236.1 KB | Display | |
Data in XML | emd_2761_validation.xml.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2761 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2761 | HTTPS FTP |
-Related structure data
Related structure data | 4udfMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_2761.map.gz / Format: CCP4 / Size: 15.1 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of human parechovirus 1 in complex with Fab fragments of AM28 human monoclonal antibody | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Human parechovirus in complex with Fab fragment of human monoclon...
Entire | Name: Human parechovirus in complex with Fab fragment of human monoclonal antibody AM28 |
---|---|
Components |
|
-Supramolecule #1000: Human parechovirus in complex with Fab fragment of human monoclon...
Supramolecule | Name: Human parechovirus in complex with Fab fragment of human monoclonal antibody AM28 type: sample / ID: 1000 / Number unique components: 2 |
---|
-Supramolecule #1: Human parechovirus 1
Supramolecule | Name: Human parechovirus 1 / type: virus / ID: 1 / Name.synonym: HPeV1 Details: Fab fragments of human monoclonal antibody, AM28 were attached to the virus NCBI-ID: 12063 / Sci species name: Human parechovirus 1 / Sci species strain: 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: HPeV1 |
---|---|
Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
-Macromolecule #1: human monoclonal antibody
Macromolecule | Name: human monoclonal antibody / type: protein_or_peptide / ID: 1 / Name.synonym: AM28 Details: Fab fragments of human monoclonal antibody, AM28 were attached to the virus Number of copies: 60 / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: 293T cells |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 10 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM MgCl2 |
---|---|
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Date | Feb 1, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 65 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.06 µm / Nominal defocus min: 1.65 µm / Nominal magnification: 69000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |