9RRS | pdb_00009rrs

AAV8 capsid in complex with Rep40 and ADP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural basis for Rep-mediated adeno-associated virus packaging.

Xu, V.McInnes, A.Wake, M.Acebron-Garcia-de-Eulate, M.Barritt, J.D.Bubeck, D.Rouse, S.L.

(2026) Cell Rep 45: 117044-117044

  • DOI: https://doi.org/10.1016/j.celrep.2026.117044
  • Primary Citation Related Structures: 
    9RM5, 9RQT, 9RRS, 9RWG, 9S0N, 9S10

  • PubMed Abstract: 

    Adeno-associated viruses (AAVs) are parvoviruses utilized as gene therapy vectors. However, the AAV packaging mechanism is unresolved at the molecular level, creating a bottleneck for vector manufacturing, safety, and efficacy. Here, cryo-EM structures of the Rep helicase packaging motor in complex with the packaging marker DNA (ITR) and the Rep-AAV8 capsid complex are presented. Rep-ITR complexes reveal dynamic oligomeric states on the DNA, elucidating the strand separation mechanism coupled to its ATPase cycle. We observe Rep preferentially bound to empty capsids, with a binding interface likely conserved across the virus family. This complex also unveils a cryptic capsid ATP-binding site which, alongside Rep binding, triggers structural rearrangements priming the capsid for packaging. Collectively, these findings advance the understanding of Rep-mediated packaging, with significant implications for parvovirus virology and viral vector design.


  • Organizational Affiliation
    • Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; AstraZeneca, Discovery Sciences, BioPharmaceuticals R&D Unit, Cambridge CB2 0AA, UK.

Macromolecule Content 

  • Total Structure Weight: 126.43 kDa 
  • Atom Count: 4,612 
  • Modeled Residue Count: 548 
  • Deposited Residue Count: 1,135 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein Rep40397adeno-associated virus 2Mutation(s): 0 
Gene Names: Rep40
EC: 3.6.4.12
UniProt
Find proteins for Q89269 (Adeno-associated virus 2 (isolate Srivastava/1982))
Explore Q89269 
Go to UniProtKB:  Q89269
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89269
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein738adeno-associated virus 8Mutation(s): 0 
UniProt
Find proteins for Q8JQF8 (Adeno-associated virus 8)
Explore Q8JQF8 
Go to UniProtKB:  Q8JQF8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JQF8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.4.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-04
    Type: Initial release
  • Version 1.1: 2026-03-18
    Changes: Data collection, Database references