9UMB | pdb_00009umb

Structure of Modified adeno-associated viral vector, AAV5-BCD

• PDB DOI: https://doi.org/10.2210/pdb9UMB/pdb
• EM Map EMD-64272: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): adeno-associated virus 5
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-04-21 Released: 2025-04-30 
• Deposition Author(s): Zhang, H., Burtseva, A.D., Strelkova, A.N., Perepelkina, M.P., Iurlova, E.V., Gershovich, P.M., Prokof'ev, A.V., Kolesnichenko, A.S., Gulnova, A.R., Nurtdinov, R.F., Vasilev, A.A., Yakovlev, P.A., Popov, V.O., Boyko, K.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.55 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of Modified adeno-associated viral vector, AAV5-BCD

Zhang, H., Burtseva, A., Boyko, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 4,828.04 kDa 
• Atom Count: 246,600 
• Modeled Residue Count: 30,960 
• Deposited Residue Count: 43,440 
• 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]	724	adeno-associated virus 5	Mutation(s): 0  Gene Names: cap, VP1
UniProt
Find proteins for Q9YIJ1 (adeno-associated virus 5) Explore Q9YIJ1  Go to UniProtKB:  Q9YIJ1

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.55 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	REFMAC	5.8.0430

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-30 
Deposition Author(s): Zhang, H., Burtseva, A.D., Strelkova, A.N., Perepelkina, M.P., Iurlova, E.V., Gershovich, P.M., Prokof'ev, A.V., Kolesnichenko, A.S., Gulnova, A.R., Nurtdinov, R.F., Vasilev, A.A., Yakovlev, P.A., Popov, V.O., Boyko, K.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release