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- PDB-6gg0: Cryo-EM structure of BK polyomavirus like particle in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6gg0
TitleCryo-EM structure of BK polyomavirus like particle in complex with single chain antibody ScFv41F17
Components
  • Capsid protein VP1
  • Heavy chain
  • light chain
KeywordsVIRUS LIKE PARTICLE / BK polyoma virus / Single chain antibody / cross neutralizing antibody
Function / homologyCapsid protein VP1,Polyomavirus / Double-stranded DNA virus, group I, capsid / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity / Capsid protein VP1
Function and homology information
Specimen sourceBK polyomavirus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.24 Å resolution
AuthorsSrinivas, H.
CitationJournal: Immunity / Year: 2019
Title: Human Memory B Cells Harbor Diverse Cross-Neutralizing Antibodies against BK and JC Polyomaviruses.
Authors: John M Lindner / Vanessa Cornacchione / Atul Sathe / Celine Be / Honnappa Srinivas / Elodie Riquet / Xavier-Charles Leber / Andreas Hein / Matthias B Wrobel / Meike Scharenberg / Thomas Pietzonka / Christian Wiesmann / Johanna Abend / Elisabetta Traggiai
Abstract: Human polyomaviruses cause a common childhood infection worldwide and typically elicit a neutralizing antibody and cellular immune response, while establishing a dormant infection in the kidney with ...Human polyomaviruses cause a common childhood infection worldwide and typically elicit a neutralizing antibody and cellular immune response, while establishing a dormant infection in the kidney with minimal clinical manifestations. However, viral reactivation can cause severe pathology in immunocompromised individuals. We developed a high-throughput, functional antibody screen to examine the humoral response to BK polyomavirus. This approach enabled the isolation of antibodies from all peripheral B cell subsets and revealed the anti-BK virus antibody repertoire as clonally complex with respect to immunoglobulin sequences and isotypes (both IgM and IgG), including a high frequency of monoclonal antibodies that broadly neutralize BK virus subtypes and the related JC polyomavirus. Cryo-electron microscopy of a broadly neutralizing IgG single-chain variable fragment complexed with BK virus-like particles revealed the quaternary nature of a conserved viral epitope at the junction between capsid pentamers. These features unravel a potent modality for inhibiting polyomavirus infection in kidney transplant recipients and other immunocompromised patients.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 2, 2018 / Release: Mar 6, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 6, 2019Structure modelrepositoryInitial release
1.1Mar 13, 2019Structure modelData collection / Database referencescitation / citation_author / em_admin / pdbx_database_proc_citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update
1.2Mar 27, 2019Structure modelData collection / Database referencescitation / database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_database_proc_citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-4398
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-4398
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Capsid protein VP1
2: Capsid protein VP1
3: Capsid protein VP1
4: Capsid protein VP1
5: Capsid protein VP1
6: Capsid protein VP1
H: Heavy chain
L: light chain


Theoretical massNumber of molelcules
Total (without water)266,1678
Polyers266,1678
Non-polymers00
Water0
1
1: Capsid protein VP1
2: Capsid protein VP1
3: Capsid protein VP1
4: Capsid protein VP1
5: Capsid protein VP1
6: Capsid protein VP1
H: Heavy chain
L: light chain
x 60


Theoretical massNumber of molelcules
Total (without water)15,970,004480
Polyers15,970,004480
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
1: Capsid protein VP1
2: Capsid protein VP1
3: Capsid protein VP1
4: Capsid protein VP1
5: Capsid protein VP1
6: Capsid protein VP1
H: Heavy chain
L: light chain
x 5


  • icosahedral pentamer
  • 1.33 MDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)1,330,83440
Polyers1,330,83440
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: Capsid protein VP1
2: Capsid protein VP1
3: Capsid protein VP1
4: Capsid protein VP1
5: Capsid protein VP1
6: Capsid protein VP1
H: Heavy chain
L: light chain
x 6


  • icosahedral 23 hexamer
  • 1.6 MDa, 48 polymers
Theoretical massNumber of molelcules
Total (without water)1,597,00048
Polyers1,597,00048
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

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Components

#1: Protein/peptide
Capsid protein VP1 /


Mass: 40184.641 Da / Num. of mol.: 6 / Source: (gene. exp.) BK polyomavirus / Gene: VP1, vp1, BK1035_00004, BK1055_00004 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q65613
#2: Protein/peptide Heavy chain


Mass: 13339.808 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide light chain /


Mass: 11719.086 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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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

Component
IDNameTypeEntity IDParent IDSource
1BK polyomavirus like particle in complex with single chain antibody ScFv41F17COMPLEX1,2,30MULTIPLE SOURCES
2BK polyomavirus like particleCOMPLEX11RECOMBINANT
3antibody ScFv41F17COMPLEX2,31RECOMBINANT
Molecular weightValue: 13.8 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
221891762BK polyomavirus
339606Homo sapiens (human)
Source (recombinant)
IDEntity assembly IDCellNcbi tax IDOrganism
22sf9 cells7108Spodoptera frugiperda (fall armyworm)
33562Escherichia coli (E. coli)
Buffer solutionDetails: 25mM Tris-HCl pH8.0 100mM NaCl / pH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 1.1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
CTF correctionType: NONE
Particle selectionNumber of particles selected: 10000
3D reconstructionResolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 6000 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00818187
ELECTRON MICROSCOPYf_angle_d1.23824682
ELECTRON MICROSCOPYf_dihedral_angle_d7.87211046
ELECTRON MICROSCOPYf_chiral_restr0.0692705
ELECTRON MICROSCOPYf_plane_restr0.0093266

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