+Open data
-Basic information
Entry | Database: PDB / ID: 7lnk | ||||||
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Title | Gorilla Bocavirus 1 Capsid | ||||||
Components | Capsid proteinCapsid | ||||||
Keywords | VIRUS / Icosahedral Capsid / Gorilla Bocavirus / GBoV / Parvovirus | ||||||
Function / homology | Parvovirus 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 species | Bocavirus gorilla/GBoV1/2009 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å | ||||||
Authors | Yu, J.C. / Mietzsch, M. / Agbandje-McKenna, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7lnk.cif.gz | 5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7lnk.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7lnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/7lnk ftp://data.pdbj.org/pub/pdb/validation_reports/ln/7lnk | HTTPS FTP |
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-Related structure data
Related structure data | 23460MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 57548.246 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bocavirus gorilla/GBoV1/2009 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D9ZK39 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Gorilla bocavirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Gorilla bocavirus |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9 |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.10-2155_2155: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168565 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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