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- PDB-38ok: AAV2 Rep68(delta1-209)/capsid/DNA complex -

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Basic information

Entry
Database: PDB / ID: 38ok
TitleAAV2 Rep68(delta1-209)/capsid/DNA complex
Components
  • Capsid protein VP1
  • Protein Rep68
  • ssDNA
KeywordsVIRUS / virion / replicase
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 / host cell nucleolus / DNA helicase activity / endonuclease activity / clathrin-dependent endocytosis of virus by host cell / DNA helicase ...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 / host cell nucleolus / DNA helicase activity / endonuclease activity / clathrin-dependent endocytosis of virus by host cell / DNA helicase / DNA replication / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / DNA binding / metal ion binding / ATP 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 / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / PYROPHOSPHATE 2- / DNA / Protein Rep68 / Capsid protein VP1
Similarity search - Component
Biological speciesAdeno-associated virus 2 Srivastava/1982
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsKaelber, J.T. / Barnakov, V. / Shen, J. / Escalante, C.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI190168 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124204 United States
CitationJournal: To Be Published
Title: Insights into the AAV packaging mechanism: Cryo-EM Structure of the AAV2 Rep-Capsid Packaging Complex
Authors: Kaelber, J.T. / Barnakov, V. / Shen, J. / Hernandez, K. / Tarbox, H.J. / Khan, A. / Escalante, C.R.
History
DepositionSep 9, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / 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 Rep68
B: Protein Rep68
C: Protein Rep68
D: Protein Rep68
E: Protein Rep68
F: Protein Rep68
G: ssDNA
V: Capsid protein VP1
W: Capsid protein VP1
X: Capsid protein VP1
Y: Capsid protein VP1
Z: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)484,66033
Polymers479,77712
Non-polymers4,88321
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 11 molecules ABCDEFVWXYZ

#1: Protein
Protein Rep68


Mass: 31403.645 Da / Num. of mol.: 6 / Mutation: del1-209
Source method: isolated from a genetically manipulated source
Details: Deletion construct lacking residues 1-209 from AAV2 rep68
Source: (gene. exp.) Adeno-associated virus 2 Srivastava/1982
Gene: Rep68 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03132, DNA helicase
#3: Protein
Capsid protein VP1


Mass: 58027.895 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus 2 Srivastava/1982
Gene: VP1 / Plasmid: pRCap / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P03135

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DNA chain , 1 types, 1 molecules G

#2: DNA chain ssDNA


Mass: 1215.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 21 molecules

#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#7: 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.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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Details

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: adeno-associated virus 2 / Type: VIRUS / Entity ID: #1, #3 / Source: RECOMBINANT
Molecular weightValue: 6.2 MDa / Experimental value: NO
Source (natural)Organism: adeno-associated virus 2 / Strain: Srivastava/1982
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293 / Plasmid: pRCap
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 280 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4 / Details: PBS plus ATPgammaS and MgCl2
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mMsodium chlorideNaCl1
22.7 mMpotassium chlorideKCl1
310 mMsodium phosphate dibasicNa2HPO41
41.8 mMpotassium phosphate monobasicKH2PO41
55 mMmagnesium chlorideMgCl21
65 mMATPgammaSC10H12N5O12P3S1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 297 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: 130000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 64.96 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 21603
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2PHENIXdev_6010model refinement
5cryoSPARC4.5.3CTF correction
10cryoSPARC4.5.3initial Euler assignment
11cryoSPARC4.5.3final Euler assignment
12cryoSPARC4.5.3classification
13cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 73031
Details: template picking of icosahedral particles, before symmetry expansion
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249955 / Algorithm: FOURIER SPACE / Details: symmetry-expanded particles post-classification / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 12KG

12kg
PDB Unreleased entry


Accession code: 12KG / Source name: PDB / Type: experimental model

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