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- PDB-9rrs: AAV8 capsid in complex with Rep40 and ADP -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9rrs
TitleAAV8 capsid in complex with Rep40 and ADP
Components
  • Capsid protein
  • Protein Rep40
KeywordsVIRUS / Adeno-associated virus / AAV / AAA+ ATPase
Function / homology
Function and homology information


T=1 icosahedral viral capsid / DNA helicase activity / viral genome replication / DNA helicase / DNA replication / nucleotide binding / host cell nucleus / structural molecule activity / 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. / 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 Rep40 / Capsid protein
Similarity search - Component
Biological speciesadeno-associated virus 2
adeno-associated virus 8
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.88 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
DepositionJun 28, 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: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4334
Polymers125,9822
Non-polymers4522
Water3,909217
1
A: Protein Rep40
B: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,586,009240
Polymers7,558,918120
Non-polymers27,090120
Water2,162120
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Protein Rep40
B: Capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 632 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)632,16720
Polymers629,91010
Non-polymers2,25810
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Protein Rep40
B: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 759 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)758,60124
Polymers755,89212
Non-polymers2,70912
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Protein Rep40


Mass: 44148.922 Da / Num. of mol.: 1
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: Protein Capsid protein


Mass: 81833.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) adeno-associated virus 8 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8JQF8
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
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
IDNameTypeEntity IDParent-IDSourceDetails
1adeno-associated virus 8VIRUS#1-#20RECOMBINANT
2AAV2 Rep40COMPLEX#11RECOMBINANTSegments of capsid-bound Rep40 aligned with the capsid icosahedral symmetry
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21adeno-associated virus 8202813
32adeno-associated virus 210804
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Homo sapiens (human)9606HEK293
32Escherichia coli (E. coli)562HEK293
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
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
3D reconstructionResolution: 1.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125371 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6v12

6v12


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

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