9RWG | pdb_00009rwg

Pentameric AAV2 Rep40 in complex with AAV8


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Rep68P [auth a],
Q [auth b],
R [auth c],
S [auth d],
T [auth e]
397adeno-associated virus 8Mutation(s): 0 
Gene Names: Rep68
EC: 3.6.4.12
UniProt
Find proteins for P03132 (Adeno-associated virus 2 (isolate Srivastava/1982))
Explore P03132 
Go to UniProtKB:  P03132
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03132
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth H]
CA [auth Q]
EA [auth R]
GA [auth U]
IA [auth V]
AA [auth H],
CA [auth Q],
EA [auth R],
GA [auth U],
IA [auth V],
KA [auth W],
MA [auth X],
OA [auth c],
PA [auth e],
U [auth A],
W [auth F],
Y [auth G]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth H]
DA [auth Q]
FA [auth R]
HA [auth U]
JA [auth V]
BA [auth H],
DA [auth Q],
FA [auth R],
HA [auth U],
JA [auth V],
LA [auth W],
NA [auth X],
V [auth A],
X [auth F],
Z [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.4.1

Structure Validation

View Full Validation Report



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