9RM5 | pdb_00009rm5

Hexameric AAV2 Rep40-ssDNA (ITR) complex in presence of ATPyS


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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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
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 nucleic acids by:  Sequence  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNAG [auth s]10adeno-associated virus 2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
H [auth a],
J [auth b],
L [auth c],
N [auth d]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
P [auth e],
R [auth f]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
I [auth a],
K [auth b],
M [auth c],
O [auth d],
Q [auth e]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.1
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited Kingdom--
Other privateUnited Kingdom--

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