7LNK | pdb_00007lnk

Gorilla Bocavirus 1 Capsid

• PDB DOI: https://doi.org/10.2210/pdb7LNK/pdb
• EM Map EMD-23460: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Bocavirus gorilla/GBoV1/2009
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-02-07 Released: 2021-03-17 
• Deposition Author(s): Yu, J.C., Mietzsch, M., Agbandje-McKenna, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.76 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Characterization of the GBoV1 Capsid and Its Antibody Interactions.

Yu, J.C., Mietzsch, M., Singh, A., Jimenez Ybargollin, A., Kailasan, S., Chipman, P., Bhattacharya, N., Fakhiri, J., Grimm, D., Kapoor, A., Kucinskaite-Kodze, I., Zvirbliene, A., Soderlund-Venermo, M., McKenna, R., Agbandje-McKenna, M.

(2021) Viruses 13

• PubMed: 33672786 
• DOI: https://doi.org/10.3390/v13020330
• Primary Citation Related Structures: 
  7LNK


• PubMed 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) 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.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Center for Structural Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
Biological Science Imaging Resource, Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA.
Department of Infectious Diseases/Virology, Medical Faculty, BioQuant, University of Heidelberg, 69120 Heidelberg, Germany.
Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43220, USA.
Department of Immunology and Cell Biology of the Institute of Biotechnology of Vilnius University, 10257 Vilnius, Lithuania.
Department of Virology, University of Helsinki, 00014 Helsinki, Finland.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3,452.89 kDa 
• Atom Count: 243,540 
• Modeled Residue Count: 30,600 
• Deposited Residue Count: 30,600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, AA [auth a], AB [auth 1], B, BA [auth b], BB [auth 2], C, CA [auth c], CB [auth 3], D, DA [auth d], DB [auth 4], E, EA [auth e], EB [auth 5], F, FA [auth f], FB [auth 6], G, GA [auth g], GB [auth 7], H, HA [auth h], HB [auth 8], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth y], Z, ZA [auth z]	510	Bocavirus gorilla/GBoV1/2009	Mutation(s): 0
UniProt
Find proteins for D9ZK39 (Bocavirus gorilla/GBoV1/2009) Explore D9ZK39  Go to UniProtKB:  D9ZK39

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.76 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cisTEM

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Yu, J.C., Mietzsch, M., Agbandje-McKenna, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM082946

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2025-05-14
  Changes: Data collection, Structure summary