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- EMDB-54050: Hexameric AAV2 Rep40-ssDNA (ITR) complex in presence of ATPyS -

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Basic information

Entry
Database: EMDB / ID: EMD-54050
TitleHexameric AAV2 Rep40-ssDNA (ITR) complex in presence of ATPyS
Map data
Sample
  • Complex: AAV2 Hexameric Rep40-ssITR in presence of ATPgS
    • Protein or peptide: Protein Rep40
    • DNA: DNA
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsHelicase / Adeno-associated Virus / AAA+ ATPase / DNA BINDING PROTEIN
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
Biological speciesadeno-associated virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.44 Å
AuthorsRouse SL / Bubeck D / Barritt JD / Xu V / Wake M
Funding support United Kingdom, 2 items
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 JD / Bubeck D / Rouse SL
History
DepositionJun 17, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54050.png

Downloads & links

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Map

FileDownload / File: emd_54050.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297. Å		0.83 Å/pix.
x 360 pix.
= 297. Å		0.83 Å/pix.
x 360 pix.
= 297. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0393
Minimum - Maximum-0.10550567 - 0.33213812
Average (Standard dev.)-0.00007065609 (±0.0072635706)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Phenix auto-sharpened map

Fileemd_54050_additional_1.map
AnnotationPhenix auto-sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54050_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54050_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AAV2 Hexameric Rep40-ssITR in presence of ATPgS

EntireName: AAV2 Hexameric Rep40-ssITR in presence of ATPgS
Components
  • Complex: AAV2 Hexameric Rep40-ssITR in presence of ATPgS
    • Protein or peptide: Protein Rep40
    • DNA: DNA
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: AAV2 Hexameric Rep40-ssITR in presence of ATPgS

SupramoleculeName: AAV2 Hexameric Rep40-ssITR in presence of ATPgS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Adeno-associated Virus 2 Replication protein 40 in complex with inverted-terminal-repeat ssDNA and ATP-gamma-S
Source (natural)Organism: adeno-associated virus 2

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Macromolecule #1: Protein Rep40

MacromoleculeName: Protein Rep40 / type: protein_or_peptide / ID: 1 / Details: Latch-WTAAV2Rep40-TrB-3xFLAG-TEV-6xHis / Number of copies: 6 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: adeno-associated virus 2
Molecular weightTheoretical: 44.148922 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EQNKENQNPN SDAPVIRSKT SARYMELVGW LVDKGITSEK QWIQEDQASY ISFNAASNSR SQIKAALDNA GKIMSLTKTA PDYLVGQQP VEDISSNRIY KILELNGYDP QYAASVFLGW ATKKFGKRNT IWLFGPATTG KTNIAEAIAH TVPFYGCVNW T NENFPFND ...String:
EQNKENQNPN SDAPVIRSKT SARYMELVGW LVDKGITSEK QWIQEDQASY ISFNAASNSR SQIKAALDNA GKIMSLTKTA PDYLVGQQP VEDISSNRIY KILELNGYDP QYAASVFLGW ATKKFGKRNT IWLFGPATTG KTNIAEAIAH TVPFYGCVNW T NENFPFND CVDKMVIWWE EGKMTAKVVE SAKAILGGSK VRVDQKCKSS AQIDPTPVIV TSNTNMCAVI DGNSTTFEHQ QP LQDRMFK FELTRRLDHD FGKVTKQEVK DFFRWAKDHV VEVEHEFYVK KGGAKKRPAP SDADISEPKR VRESVAQPST SDA EASINY ADRLARGHSL GSLVPRGSGG GGSGGGGSGG GGSMDYKDHD GDYKDHDIDY KDDDDKGSEN LYFQSHHHHH H

UniProtKB: Protein Rep40

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Macromolecule #2: DNA

MacromoleculeName: DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: adeno-associated virus 2
Molecular weightTheoretical: 2.846861 KDa
SequenceString:
(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 4 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
200.0 mMNaClSodium Chloride
25.0 mM(HOCH2)*3CNH2Tris
1.0 mMC9H15O6PTCEP
1.0 %C3H8O3Glycerol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU (ver. 3.8.1)
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average exposure time: 1.68 sec. / Average electron dose: 39.99 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 91099
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: ISOLDE (ver. 1.8)
Output model

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

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