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- EMDB-4398: Cryo-EM structure of BK polyomavirus like particle in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-4398
TitleCryo-EM structure of BK polyomavirus like particle in complex with single chain antibody ScFv41F17
Map data
Sample
  • Complex: BK polyomavirus like particle in complex with single chain antibody ScFv41F17
    • Complex: BK polyomavirus like particle
      • Protein or peptide: Capsid protein VP1
    • Complex: antibody ScFv41F17
      • Protein or peptide: Heavy chain
      • Protein or peptide: light chain
KeywordsBK polyoma virus / Single chain antibody / cross neutralizing antibody / VIRUS LIKE PARTICLE
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)
Methodsingle 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, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseMar 6, 2019-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6gg0
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6gg0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4398.png

Downloads & links

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Map

FileDownload / File: emd_4398.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 580 pix.
= 649.6 Å		1.12 Å/pix.
x 580 pix.
= 649.6 Å		1.12 Å/pix.
x 580 pix.
= 649.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.057476763 - 0.09363829
Average (Standard dev.)0.0010663574 (±0.005737116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions580580580
Spacing580580580
CellA=B=C: 649.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z580580580
origin x/y/z0.0000.0000.000
length x/y/z649.600649.600649.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS580580580
D min/max/mean-0.0570.0940.001

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Supplemental data

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Sample components

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Entire : BK polyomavirus like particle in complex with single chain antibo...

EntireName: BK polyomavirus like particle in complex with single chain antibody ScFv41F17
Components
  • Complex: BK polyomavirus like particle in complex with single chain antibody ScFv41F17
    • Complex: BK polyomavirus like particle
      • Protein or peptide: Capsid protein VP1
    • Complex: antibody ScFv41F17
      • Protein or peptide: Heavy chain
      • Protein or peptide: light chain

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Supramolecule #1: BK polyomavirus like particle in complex with single chain antibo...

SupramoleculeName: BK polyomavirus like particle in complex with single chain antibody ScFv41F17
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 13.8 MDa

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Supramolecule #2: BK polyomavirus like particle

SupramoleculeName: BK polyomavirus like particle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: BK polyomavirus

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Supramolecule #3: antibody ScFv41F17

SupramoleculeName: antibody ScFv41F17 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: BK polyomavirus
Molecular weightTheoretical: 40.184641 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAPTKRKGEC PGAAPKKPKE PVQVPKLLIK GGVEVLEVKT GVDAITEVEC FLNPEMGDPD ENLRGFSLKL SAENDFSSDS PERKMLPCY STARIPLPNL NEDLTCGNLL MWEAVTVQTE VIGITSMLNL HAGSQKVHEH GGGKPIQGSN FHFFAVGGDP L EMQGVLMN ...String:
MAPTKRKGEC PGAAPKKPKE PVQVPKLLIK GGVEVLEVKT GVDAITEVEC FLNPEMGDPD ENLRGFSLKL SAENDFSSDS PERKMLPCY STARIPLPNL NEDLTCGNLL MWEAVTVQTE VIGITSMLNL HAGSQKVHEH GGGKPIQGSN FHFFAVGGDP L EMQGVLMN YRTKYPDGTI TPKNPTAQSQ VMNTDHKAYL DKNNAYPVEC WVPDPSRNEN TRYFGTFTGG ENVPPVLHVT NT ATTVLLD EQGVGPLCKA DSLYVSAADI CGLFTNSSGT QQWRGLARYF KIRLRKRSVK NPYPISFLLS DLINRRTQRV DGQ PMYGME SQVEEVRVFD GTERLPGDPD MIRYIDKQGQ LQTKML

UniProtKB: Capsid protein VP1

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Macromolecule #2: Heavy chain

MacromoleculeName: Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.339808 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGPG LVKPSQTLSL TCTVSGGSIS GGGYYWSWIR QHPGKGLEFI GYIYYNRGTY YNPALKSRLT ISVDTSKNDF SLKLSSVSA ADTAVYYCAR CVLGGYGSDA FDRWGQGTTV TVSSG

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Macromolecule #3: light chain

MacromoleculeName: light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.719086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EIVLTQSPVT LSLSPGERAI LSCRASQSVS SHLAWYQQKP GQAPRLLIYD ASSRANGIPA RFSGSGSGTD FTLTISSLAP EDFAVYYCQ QRSSWPPSLT FGGGTKVEIR

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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 / Details: 25mM Tris-HCl pH8.0 100mM NaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10000
CTF correctionType: NONE
Startup modelType of model: NONE / Details: A sphere was used as an initial model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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