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- EMDB-9110: Structure of parvovirus B19 decorated with Fab molecules from a h... -

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Basic information

Entry
Database: EMDB / ID: EMD-9110
TitleStructure of parvovirus B19 decorated with Fab molecules from a human antibody
Map dataMap of B19-Fab complex, reconstructed in jspr and postprocessed in RELION. Sharpened and low-pass filtered to 3A.
Sample
  • Complex: Complex of B19 VLP with Fab molecules of antibody 860-55D
    • Complex: antibody 860-55D Fab
      • Protein or peptide: antibody 860-55D heavy chain
      • Protein or peptide: antibody 860-55D light chain
    • Virus: Human parvovirus B19
      • Protein or peptide: VP2
Function / homologyPhospholipase 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 speciesHomo sapiens (human) / Human parvovirus B19
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRossmann MG / Sun Y / Klose T / Liu Y
CitationJournal: 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
DepositionSep 10, 2018-
Header (metadata) releaseOct 3, 2018-
Map releaseOct 3, 2018-
UpdateFeb 13, 2019-
Current statusFeb 13, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nn3
  • Surface level: 9
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6nn3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9110.png

Downloads & links

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Map

FileDownload / File: emd_9110.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of B19-Fab complex, reconstructed in jspr and postprocessed in RELION. Sharpened and low-pass filtered to 3A.
Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 9.0 / Movie #1: 9
Minimum - Maximum-81.878870000000006 - 131.670780000000008
Average (Standard dev.)0.05495324 (±3.757855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 561.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z561.600561.600561.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-81.879131.6710.055

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Supplemental data

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Half map: Half map 1 with spherical mask

Fileemd_9110_half_map_1.map
AnnotationHalf map 1 with spherical mask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 with spherical mask

Fileemd_9110_half_map_2.map
AnnotationHalf map 2 with spherical mask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of B19 VLP with Fab molecules of antibody 860-55D

EntireName: Complex of B19 VLP with Fab molecules of antibody 860-55D
Components
  • Complex: Complex of B19 VLP with Fab molecules of antibody 860-55D
    • Complex: antibody 860-55D Fab
      • Protein or peptide: antibody 860-55D heavy chain
      • Protein or peptide: antibody 860-55D light chain
    • Virus: Human parvovirus B19
      • Protein or peptide: VP2

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Supramolecule #1: Complex of B19 VLP with Fab molecules of antibody 860-55D

SupramoleculeName: Complex of B19 VLP with Fab molecules of antibody 860-55D
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 5.6 MDa

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Supramolecule #3: antibody 860-55D Fab

SupramoleculeName: antibody 860-55D Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #2: Human parvovirus B19

SupramoleculeName: 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
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human parvovirus B19
Molecular weightTheoretical: 60.916016 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: antibody 860-55D heavy chain

MacromoleculeName: antibody 860-55D heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.756069 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVAASDTLSL TCTVSGGSLA AAFYWSWIRQ APGKGLEWIG YIYYSGSAYY SPSLESRVTM SDAAAAAAAA AAAAAAAAV YYCVRAAAAA AAAAAAAFAS WGQGTLVTV

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Macromolecule #3: antibody 860-55D light chain

MacromoleculeName: antibody 860-55D light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.895869 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AAALTQPLSV SVSPGQTAIF TCSGDNLGDK YVYWFQQRPG QSPALLIYQD NKRPSGIPER FSGSNSGNTA TLTISGTQST DEADYYCQT WDSTVVFGGG TKL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 295 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9120
CTF correctionSoftware:
Namedetails
CTFFINDdetermination
JALIGNrefinement
Startup modelType of model: OTHER / Details: Randomly generated from 200 particles using jspr
Initial angle assignmentType: OTHER / Software - Name: JALIGN
Final 3D classificationNumber classes: 50 / Avg.num./class: 180 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: JALIGN
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: J3DR / Number images used: 7395
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 100
Output model

PDB-6nn3:
Structure of parvovirus B19 decorated with Fab molecules from a human antibody

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