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- PDB-9rm5: Hexameric AAV2 Rep40-ssDNA (ITR) complex in presence of ATPyS -

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Basic information

Entry
Database: PDB / ID: 9rm5
TitleHexameric AAV2 Rep40-ssDNA (ITR) complex in presence of ATPyS
Components
  • DNA
  • Protein Rep40
KeywordsDNA BINDING PROTEIN / Helicase / Adeno-associated Virus / AAA+ ATPase
Function / homology
Function and homology information


DNA helicase activity / viral genome replication / DNA helicase / DNA replication / host cell nucleus / ATP hydrolysis activity / ATP binding
Similarity search - Function
Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / Protein Rep40
Similarity search - Component
Biological speciesadeno-associated virus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.44 Å
AuthorsRouse, S.L. / Bubeck, D. / Barritt, J.D. / Xu, V. / Wake, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Other government United Kingdom
Other private United Kingdom
CitationJournal: To Be Published
Title: Dynamic oligomerisation states of replicative helicase 40 coordinate during adeno-associated virus packaging
Authors: Xu, V. / Barritt, J.D. / Bubeck, D. / Rouse, S.L.
History
DepositionJun 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: Protein Rep40
b: Protein Rep40
c: Protein Rep40
d: Protein Rep40
e: Protein Rep40
f: Protein Rep40
s: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,80918
Polymers267,7407
Non-polymers3,06911
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Protein Rep40


Mass: 44148.922 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Latch-WTAAV2Rep40-TrB-3xFLAG-TEV-6xHis / Source: (gene. exp.) adeno-associated virus 2 / Gene: Rep40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q89269, DNA helicase
#2: DNA chain DNA


Mass: 2846.861 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) adeno-associated virus 2
#3: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: AAV2 Hexameric Rep40-ssITR in presence of ATPgS / Type: COMPLEX
Details: Adeno-associated Virus 2 Replication protein 40 in complex with inverted-terminal-repeat ssDNA and ATP-gamma-S
Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: adeno-associated virus 2
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMSodium ChlorideNaCl1
225 mMTris(HOCH2)*3CNH21
31 mMTCEPC9H15O6P1
41 %GlycerolC3H8O31
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.68 sec. / Electron dose: 39.99 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2EPU3.8.1image acquisition
4cryoSPARC4.4.1CTF correction
7ISOLDE1.8model fitting
10cryoSPARC4.4.1final Euler assignment
12cryoSPARC4.4.13D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91099 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

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