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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 / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Major capsid protein VP1 / Capsid protein VP1
Similarity search - Component
Biological speciesBK polyomavirus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.24 Å
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 ...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.
History
DepositionMay 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
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Revision 1.0Mar 6, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Mar 13, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update
Revision 1.2Mar 27, 2019Group: Data collection / Database references
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Revision 1.3Dec 11, 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 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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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
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  • Simplified surface model + fitted atomic model
  • EMDB-4398
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  • Superimposition on EM map
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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
Polymers266,1678
Non-polymers00
Water00
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
Polymers15,970,004480
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Polymers1,330,83440
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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
Polymers1,597,00048
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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
Capsid protein VP1


Mass: 40184.641 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BK polyomavirus / Gene: VP1, vp1, BK1035_00004, BK1055_00004 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q65613, UniProt: P03088*PLUS
#2: Antibody Heavy chain


Mass: 13339.808 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody light chain


Mass: 11719.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1BK polyomavirus like particle in complex with single chain antibody ScFv41F17COMPLEXall0MULTIPLE SOURCES
2BK polyomavirus like particleCOMPLEX#11RECOMBINANT
3antibody ScFv41F17COMPLEX#2-#31RECOMBINANT
Molecular weightValue: 13.8 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22BK polyomavirus1891762
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
22Spodoptera frugiperda (fall armyworm)7108sf9 cells
33Escherichia coli (E. coli)562
Buffer solutionpH: 8 / Details: 25mM Tris-HCl pH8.0 100mM NaCl
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
MicroscopyModel: 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
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 10000
3D reconstructionResolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. 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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