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- EMDB-23460: Gorilla Bocavirus 1 Capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-23460
TitleGorilla Bocavirus 1 Capsid
Map data
Sample
  • Virus: Gorilla bocavirus
    • Protein or peptide: Capsid protein
KeywordsIcosahedral Capsid / Gorilla Bocavirus / GBoV / VIRUS / Parvovirus
Function / homologyParvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / Capsid protein
Function and homology information
Biological speciesBocavirus gorilla/GBoV1/2009 / Gorilla bocavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsYu JC / Mietzsch M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: Viruses / Year: 2021
Title: Characterization of the GBoV1 Capsid and Its Antibody Interactions.
Authors: Jennifer Chun Yu / Mario Mietzsch / Amriti Singh / Alberto Jimenez Ybargollin / Shweta Kailasan / Paul Chipman / Nilakshee Bhattacharya / Julia Fakhiri / Dirk Grimm / Amit Kapoor / Indrė ...Authors: Jennifer Chun Yu / Mario Mietzsch / Amriti Singh / Alberto Jimenez Ybargollin / Shweta Kailasan / Paul Chipman / Nilakshee Bhattacharya / Julia Fakhiri / Dirk Grimm / Amit Kapoor / Indrė Kučinskaitė-Kodzė / Aurelija Žvirblienė / Maria Söderlund-Venermo / Robert McKenna / Mavis Agbandje-McKenna /
Abstract: Human bocavirus 1 (HBoV1) has gained attention as a gene delivery vector with its ability to infect polarized human airway epithelia and 5.5 kb genome packaging capacity. Gorilla bocavirus 1 (GBoV1) ...Human bocavirus 1 (HBoV1) has gained attention as a gene delivery vector with its ability to infect polarized human airway epithelia and 5.5 kb genome packaging capacity. Gorilla bocavirus 1 (GBoV1) VP3 shares 86% amino acid sequence identity with HBoV1 but has better transduction efficiency in several human cell types. Here, we report the capsid structure of GBoV1 determined to 2.76 Å resolution using cryo-electron microscopy (cryo-EM) and its interaction with mouse monoclonal antibodies (mAbs) and human sera. GBoV1 shares capsid surface morphologies with other parvoviruses, with a channel at the 5-fold symmetry axis, protrusions surrounding the 3-fold axis and a depression at the 2-fold axis. A 2/5-fold wall separates the 2-fold and 5-fold axes. Compared to HBoV1, differences are localized to the 3-fold protrusions. Consistently, native dot immunoblots and cryo-EM showed cross-reactivity and binding, respectively, by a 5-fold targeted HBoV1 mAb, 15C6. Surprisingly, recognition was observed for one out of three 3-fold targeted mAbs, 12C1, indicating some structural similarity at this region. In addition, GBoV1, tested against 40 human sera, showed the similar rates of seropositivity as HBoV1. Immunogenic reactivity against parvoviral vectors is a significant barrier to efficient gene delivery. This study is a step towards optimizing bocaparvovirus vectors with antibody escape properties.
History
DepositionFeb 7, 2021-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lnk
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7lnk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23460.png

Downloads & links

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Map

FileDownload / File: emd_23460.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.07 Å/pix.
x 400 pix.
= 428.8 Å		1.07 Å/pix.
x 400 pix.
= 428.8 Å		1.07 Å/pix.
x 400 pix.
= 428.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-11.169619000000001 - 18.197894999999999
Average (Standard dev.)0.000000003078539 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 428.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0721.0721.072
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z428.800428.800428.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ400400400
MAP C/R/S213
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-11.17018.1980.000

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Supplemental data

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Sample components

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Entire : Gorilla bocavirus

EntireName: Gorilla bocavirus
Components
  • Virus: Gorilla bocavirus
    • Protein or peptide: Capsid protein

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Supramolecule #1: Gorilla bocavirus

SupramoleculeName: Gorilla bocavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1511879 / Sci species name: Gorilla bocavirus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Bocavirus gorilla/GBoV1/2009
Molecular weightTheoretical: 57.548246 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSGVGISTGG WVGGSHFADK YVITKNTRQF ITSIQNGHLY KTEIINPSNG NGKSQRCVTT PWTYFNFNQY SCHFSPQDWQ RLTNEYKRF RPKAMLVKIY NLQIKQILSN GADTTYNNDL TAGVHIFCDG EHAYPNASHP WDEDVMPDLP YKTWKLFQYG Y IPILNELA ...String:
GSGVGISTGG WVGGSHFADK YVITKNTRQF ITSIQNGHLY KTEIINPSNG NGKSQRCVTT PWTYFNFNQY SCHFSPQDWQ RLTNEYKRF RPKAMLVKIY NLQIKQILSN GADTTYNNDL TAGVHIFCDG EHAYPNASHP WDEDVMPDLP YKTWKLFQYG Y IPILNELA DLDGTTAGGT ATEKAILYQM PFFMLENSDH EVLRTGESSE FTFNFDCEWV NNERAYIPPG LMFNPKVPTR RV QYIRQNG QTTASTSRIE PYSKPTSWMT GPGFLGGQRV GPATSDTAPY MVCTKPDGVY INTGAAGYGS GFDPPSGSLA PTD LEYKLQ WYQTPEDTGN NGNIIANPSL SMLRDQLLYR GNQTTYNLNA DVWMFPNQIW DRYPITREHP IWCKKPRADK NTII DPFDG SIAMDHPPGT IFIKMAKIPV PSSTNADSYL NIYCTGQVSC EIVWEVERYV TKNWRPERRH TALGMSIGGT ENVSP TYHV DSAGTYIQPT TFDQCMPVKT NINKVL

UniProtKB: Capsid protein

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 168565
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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