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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 / homology
Function and homology information


T=1 icosahedral viral capsid / structural molecule activity
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / 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 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman parvovirus B19
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsRossmann, M.G. / Sun, Y. / Klose, T. / Liu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1515260 United 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, 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
DepositionJan 14, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 13, 2019ID: 6MF7
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.5Mar 4, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list

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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
  • EMDB-9110
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Structure viewerMolecule:
MolmilJmol/JSmol

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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
Polymers84,9373
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
Polymers5,096,249180
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
Polymers424,68715
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
Polymers509,62518
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein VP2 of B19 parvovirus / VP1 protein


Mass: 60946.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parvovirus B19 / Gene: VP1 / Production host: unidentified baculovirus / References: UniProt: Q75U93
#2: Antibody Fab monoclonal antibody 860-55D, heavy chain


Mass: 13095.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody Fab monoclonal antibody 860-55D, light chain


Mass: 10895.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D 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: all / 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 / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: B19 VLPs were incubated with purified Fab molecules overnight at 4 degrees.
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
MicroscopyModel: 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 X / Calibrated magnification: 22500 X / 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 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 70 K
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) / Num. of grids imaged: 1 / Num. 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 selectionNum. of particles selected: 9120
3D reconstructionMethod: SINGLE PARTICLESingle particle analysis / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7395 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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