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- PDB-9rwg: Pentameric AAV2 Rep40 in complex with AAV8 -

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Basic information

Entry
Database: PDB / ID: 9rwg
TitlePentameric AAV2 Rep40 in complex with AAV8
Components
  • Capsid protein
  • Protein Rep68
KeywordsVIRUS / Adeno-associated virus / AAV / AAA+ ATPase
Function / homology
Function and homology information


symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont entry into host cell via permeabilization of host membrane / viral DNA genome replication / T=1 icosahedral viral capsid / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endonuclease activity / DNA helicase / DNA replication / nucleotide binding / host cell nucleus ...symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont entry into host cell via permeabilization of host membrane / viral DNA genome replication / T=1 icosahedral viral capsid / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endonuclease activity / DNA helicase / DNA replication / nucleotide binding / host cell nucleus / structural molecule activity / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Rep protein catalytic-like / Rep protein catalytic domain like / : / Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / 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. / Phospholipase A2-like domain / Phospholipase A2-like domain ...Rep protein catalytic-like / Rep protein catalytic domain like / : / Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / 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. / Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP1/VP2 / Capsid/spike protein, ssDNA virus / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Protein Rep68 / Capsid protein
Similarity search - Component
Biological speciesadeno-associated virus 8
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsRouse, S.L. / Bubeck, D. / Barritt, J.D. / Xu, V. / Wake, M.
Funding support2items
OrganizationGrant numberCountry
Other government
Other private
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. / Wake, M. / Rouse, S.L.
History
DepositionJul 9, 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: Mask / Part number: 1 / Data content type: Mask / 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: Capsid protein
B: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
Q: Capsid protein
R: Capsid protein
S: Capsid protein
U: Capsid protein
V: Capsid protein
W: Capsid protein
X: Capsid protein
Y: Capsid protein
a: Protein Rep68
b: Protein Rep68
c: Protein Rep68
d: Protein Rep68
e: Protein Rep68
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,453,61042
Polymers1,448,24020
Non-polymers5,36922
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
Capsid protein


Mass: 81833.047 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Details: WT AAV8 VP1/2/3 truncated to fit in map / Source: (gene. exp.) adeno-associated virus 8 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8JQF8
#2: Protein
Protein Rep68


Mass: 44148.922 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Latch-WTAAV2Rep40-TrB-3xFLAG-TEV-6xHis / Source: (gene. exp.) adeno-associated virus 8 / Gene: Rep68 / Production host: Escherichia coli (E. coli) / References: UniProt: P03132, DNA helicase
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Pentameric AAV2 Rep40 in complex with AAV8 capsidCOMPLEXFrom local refinement of 1/12 5-fold vertex of the Rep-bound AAV8 capsid#1-#20RECOMBINANT
2Pentameric AAV2 Rep40COMPLEX#21RECOMBINANT
3AAV8 capsidCOMPLEX#11RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21adeno-associated virus 8202813
32adeno-associated virus 210804
43adeno-associated virus 210804
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Homo sapiens (human)9606HEK293
32Escherichia coli (E. coli)562HEK293
43Homo sapiens (human)9606HEK293
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural host
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens9606
22Homo sapiens9606
Virus shell
IDEntity assembly-IDNameDiameter (nm)Triangulation number (T number)
11Virus protein (VP)2101
22
33
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2EPU3.8.1image acquisition
4cryoSPARC4.4.1CTF correction
7ISOLDE1.8model fitting
9PHENIXmodel refinement
11cryoSPARC4.4.1final Euler assignment
13cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191887 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6v12

6v12


Accession code: 6v12 / Source name: PDB / Type: experimental model

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