9LGJ | pdb_00009lgj

Cryo-EM structure of a designed AAV2-based vector

PDB DOI: https://doi.org/10.2210/pdb9LGJ/pdb
EM Map EMD-63067: EMDB EMDataResource

Classification: VIRUS
Organism(s): Adeno-associated virus 2 Srivastava/1982
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-01-10 Released: 2025-12-24
Deposition Author(s): Luo, S., Ke, X., Zheng, Q.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.58 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9LGJ

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of a designed AAV2-based vector

Luo, S., Ke, X., Zheng, Q.

To be published.

Macromolecule Content

Total Structure Weight: 4,971.13 kDa
Atom Count: 249,660
Modeled Residue Count: 31,200
Deposited Residue Count: 44,580
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A AA [auth BA] AB [auth BB] B BA [auth CA] A, AA [auth BA], AB [auth BB], B, BA [auth CA], BB [auth CB], C, CA [auth DA], CB [auth DB], D, DA [auth EA], DB [auth EB], E, EA [auth FA], EB [auth FB], F, FA [auth GA], FB [auth GB], G, GA [auth HA], GB [auth HB], H, HA [auth IA], HB [auth IB], I, IA [auth JA], J, JA [auth KA], K, KA [auth LA], L, LA [auth MA], M, MA [auth NA], N, NA [auth OA], O, OA [auth PA], P, PA [auth QA], Q, QA [auth RA], R, RA [auth SA], S, SA [auth TA], T, TA [auth UA], U [auth V], UA [auth VA], V [auth W], VA [auth WA], W [auth X], WA [auth XA], X [auth Y], XA [auth YA], Y [auth Z], YA [auth ZA], Z [auth AA], ZA [auth AB]	743	Adeno-associated virus 2 Srivastava/1982	Mutation(s): 2 Gene Names: VP1
UniProt
Find proteins for P03135 (Adeno-associated virus 2 (isolate Srivastava/1982)) Explore P03135 Go to UniProtKB: P03135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03135
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.58 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2025-12-24
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.