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Yorodumi- EMDB-9110: Structure of parvovirus B19 decorated with Fab molecules from a h... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9110 | |||||||||
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Title | Structure of parvovirus B19 decorated with Fab molecules from a human antibody | |||||||||
Map data | Map of B19-Fab complex, reconstructed in jspr and postprocessed in RELION. Sharpened and low-pass filtered to 3A. | |||||||||
Sample |
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Function / homology | Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / VP1 protein Function and homology information | |||||||||
Biological species | Homo sapiens (human) / Human parvovirus B19 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Rossmann MG / Sun Y / Klose T / Liu Y | |||||||||
Citation | Journal: J Virol / Year: 2019 Title: Structure of Parvovirus B19 Decorated by Fabs from a Human Antibody. Authors: Yingyuan Sun / Thomas Klose / Yue Liu / Susanne Modrow / Michael G Rossmann / Abstract: Parvovirus B19, one of the most common human pathogens, is a small DNA virus that belongs to the As a result of previous infections, antibodies to B19 are present in most adults. B19 has a strong ...Parvovirus B19, one of the most common human pathogens, is a small DNA virus that belongs to the As a result of previous infections, antibodies to B19 are present in most adults. B19 has a strong tropism to erythroid progenitor cells and is able to cause a series of medical conditions, including fifth disease, arthritis, myocarditis, hydrops fetalis, and aplastic crisis. No approved vaccine is currently available for B19, and there is a lack of structural characterization of any B19 epitopes. Here we present the first cryo-electron microscopy (cryo-EM) structure of a B19 virus-like particle (VLP) complexed with the antigen-binding fragment (Fab) of a human neutralizing antibody, 860-55D. A model was built into the 3.2-Å-resolution map, and the antigenic residues on the surface of the B19 capsid were identified. Antibody 860-55D bridges the capsid of B19 by binding to a quaternary structure epitope formed by residues from three neighboring VP2 capsid proteins. Parvovirus B19 is a common human pathogen and a particular threat to children, pregnant women, and patients with sickle cell disease or AIDS. Currently, neutralizing antibody is the most efficient treatment for acute B19 infections. Research on the antigenic properties of B19 will guide the usage of these antibodies and facilitate vaccine development. We have determined and report here the high-resolution structure of B19 virus-like particles (VLPs) complexed with the Fab of a human neutralizing antibody. The structure shows a quaternary structure epitope formed by three VP2 proteins and provides details on host recognition of human B19 virus. | |||||||||
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_9110.map.gz | 243.3 MB | EMDB map data format | |
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Header (meta data) | emd-9110-v30.xml emd-9110.xml | 21.3 KB 21.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9110_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_9110.png | 294.1 KB | ||
Others | emd_9110_half_map_1.map.gz emd_9110_half_map_2.map.gz | 37.2 MB 37.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9110 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9110 | HTTPS FTP |
-Validation report
Summary document | emd_9110_validation.pdf.gz | 615.9 KB | Display | EMDB validaton report |
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Full document | emd_9110_full_validation.pdf.gz | 615.5 KB | Display | |
Data in XML | emd_9110_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | emd_9110_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9110 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9110 | HTTPS FTP |
-Related structure data
Related structure data | 6nn3MC 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_9110.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of B19-Fab complex, reconstructed in jspr and postprocessed in RELION. Sharpened and low-pass filtered to 3A. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half map 1 with spherical mask
File | emd_9110_half_map_1.map | ||||||||||||
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Annotation | Half map 1 with spherical mask | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 with spherical mask
File | emd_9110_half_map_2.map | ||||||||||||
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Annotation | Half map 2 with spherical mask | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of B19 VLP with Fab molecules of antibody 860-55D
Entire | Name: Complex of B19 VLP with Fab molecules of antibody 860-55D |
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Components |
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-Supramolecule #1: Complex of B19 VLP with Fab molecules of antibody 860-55D
Supramolecule | Name: Complex of B19 VLP with Fab molecules of antibody 860-55D type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 5.6 MDa |
-Supramolecule #3: antibody 860-55D Fab
Supramolecule | Name: antibody 860-55D Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #2: Human parvovirus B19
Supramolecule | Name: Human parvovirus B19 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1 / NCBI-ID: 10798 / Sci species name: Human parvovirus B19 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) |
Host system | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human parvovirus B19 |
Molecular weight | Theoretical: 60.916016 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MTSVNSAEAS TGAGGGGSNP VKSMWSEGAT FSANSVTCTF SRQFLIPYDP EHHYKVFSPA ASSCHNASGK EAKVCTISPI MGYSTPWRY LDFNALNLFF SPLEFQHLIE NYGSIAPDAL TVTISEIAVK DVTDKTGGGV QVTDSTTGRL CMLVDHEYKY P YVLGQGQD ...String: MTSVNSAEAS TGAGGGGSNP VKSMWSEGAT FSANSVTCTF SRQFLIPYDP EHHYKVFSPA ASSCHNASGK EAKVCTISPI MGYSTPWRY LDFNALNLFF SPLEFQHLIE NYGSIAPDAL TVTISEIAVK DVTDKTGGGV QVTDSTTGRL CMLVDHEYKY P YVLGQGQD TLAPELPIWV YFPPQYAYLT VGDVNTQGIS GDSKKLASEE SAFYVLEHSS FQLLGTGGTA TMSYKFPPVP PE NLEGCSQ HFYEMYNPLY GSRLGVPDTL GGDPKFRSLT HEDHAIQPQN FMPGPLVNSV STKEGDSSNT GAGKALTGLS TGT SQNTRI SLRPGPVSQP YHHWDTDKYV TGINAISHGQ TTYGNAEDKE YQQGVGRFPN EKEQLKQLQG LNMHTYFPNK GTQQ YTDQI ERPLMVGSVW NRRALHYESQ LWSKIPNLDD SFKTQFAALG GWGLHQPPPQ IFLKILPQSG PIGGIKSMGI TTLVQ YAVG IMTVTMTFKL GPRKATGRWN PQPGVYPPHA AGHLPYVLYD PTATDAKQHH RHGYEKPEEL WTAKSRVHPL |
-Macromolecule #2: antibody 860-55D heavy chain
Macromolecule | Name: antibody 860-55D heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.756069 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQESGPG LVAASDTLSL TCTVSGGSLA AAFYWSWIRQ APGKGLEWIG YIYYSGSAYY SPSLESRVTM SDAAAAAAAA AAAAAAAAV YYCVRAAAAA AAAAAAAFAS WGQGTLVTV |
-Macromolecule #3: antibody 860-55D light chain
Macromolecule | Name: antibody 860-55D light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.895869 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AAALTQPLSV SVSPGQTAIF TCSGDNLGDK YVYWFQQRPG QSPALLIYQD NKRPSGIPER FSGSNSGNTA TLTISGTQST DEADYYCQT WDSTVVFGGG TKL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 20.265 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 295 K / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 0-40 / Number grids imaged: 2 / Number real images: 1759 / Average exposure time: 0.2 sec. / Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 100 |
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Output model | PDB-6nn3: |