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- PDB-6nn3: Structure of parvovirus B19 decorated with Fab molecules from a h... -

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Basic information

Entry
Database: PDB / ID: 6nn3
TitleStructure of parvovirus B19 decorated with Fab molecules from a human antibody
Components
  • Fab monoclonal antibody 860-55D, heavy chain
  • Fab monoclonal antibody 860-55D, light chain
  • VP2 of B19 parvovirus
KeywordsVIRUS LIKE PARTICLE / B19 / VP2 / antibody / epitope / VIRUS LIKE PARTICLE-IMMUNE SYSTEM complex
Function / homologyParvovirus coat protein VP2 / Parvovirus coat protein VP1, N-terminal / Capsid/spike protein, ssDNA virus / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Parvovirus coat protein VP1 / viral capsid / structural molecule activity / VP1 protein
Function and homology information
Specimen sourceHuman parvovirus B19
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.22 Å resolution
AuthorsRossmann, M.G. / Sun, Y. / Klose, T. / Liu, Y.
Funding supportUnited States , 1 items
OrganizationGrant numberCountry
National Science Foundation (United States)MCB1515260United States
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, 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-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 3.2Å resolution map and the antigenic residues on the surface of 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 of 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 structure of B19 VLPs complexed with the Fab of a human neutralizing antibody at high resolution. The structure shows a quaternary structure epitope formed by three VP2 proteins and provides details on host recognition of human B19 virus.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 14, 2019 / Release: Feb 13, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 13, 2019Structure modelrepositoryInitial release
1.1Mar 6, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-9110
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP2 of B19 parvovirus
H: Fab monoclonal antibody 860-55D, heavy chain
L: Fab monoclonal antibody 860-55D, light chain


Theoretical massNumber of molelcules
Total (without water)84,9373
Polyers84,9373
Non-polymers00
Water0
1
A: VP2 of B19 parvovirus
H: Fab monoclonal antibody 860-55D, heavy chain
L: Fab monoclonal antibody 860-55D, light chain
x 60


Theoretical massNumber of molelcules
Total (without water)5,096,249180
Polyers5,096,249180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: VP2 of B19 parvovirus
H: Fab monoclonal antibody 860-55D, heavy chain
L: Fab monoclonal antibody 860-55D, light chain
x 5


  • icosahedral pentamer
  • 425 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)424,68715
Polyers424,68715
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP2 of B19 parvovirus
H: Fab monoclonal antibody 860-55D, heavy chain
L: Fab monoclonal antibody 860-55D, light chain
x 6


  • icosahedral 23 hexamer
  • 510 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)509,62518
Polyers509,62518
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: VP2 of B19 parvovirus
H: Fab monoclonal antibody 860-55D, heavy chain
L: Fab monoclonal antibody 860-55D, light chain
x 60


  • crystal asymmetric unit, crystal frame
  • 5.1 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)5,096,249180
Polyers5,096,249180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60

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Components

#1: Protein/peptide VP2 of B19 parvovirus / VP1 protein


Mass: 60946.047 Da / Num. of mol.: 1 / Source: (gene. exp.) Human parvovirus B19 / Gene: VP1 / Production host: unidentified baculovirus / References: UniProt: Q75U93
#2: Protein/peptide Fab monoclonal antibody 860-55D, heavy chain


Mass: 13095.569 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
#3: Protein/peptide Fab monoclonal antibody 860-55D, light chain


Mass: 10895.869 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: complex of human parvovirus B19 major capsid protein VP2 with Fab molecules from a human neutralizing antibody
Type: COMPLEX / Entity ID: 1, 2, 3 / Source: MULTIPLE SOURCES
Molecular weightValue: 5.4 MDa / Experimental value: NO
Source (natural)Organism: Human parvovirus B19
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml
Details: B19 VLPs were incubated with purified Fab molecules overnight at 4 degrees.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 / Calibrated magnification: 22500 / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 kelvins / Temperature (min): 70 kelvins
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 38 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 1759
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN2particle selectione2boxer.py
2Leginonimage acquisition
4CTFFIND3CTF correction
9jsprinitial Euler assignment
10jsprfinal Euler assignment
12jspr3D reconstruction
13Cootmodel refinement
Image processingDetails: Motion corrected
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 9120
3D reconstructionMethod: SINGLE PARTICLESingle particle analysis / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 7395 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL

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