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- EMDB-54328: Pentameric AAV2 Rep40 in complex with AAV8 -

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Basic information

Entry
Database: EMDB / ID: EMD-54328
TitlePentameric AAV2 Rep40 in complex with AAV8
Map data
Sample
  • Complex: Pentameric AAV2 Rep40 in complex with AAV8 capsid
    • Complex: Pentameric AAV2 Rep40
      • Protein or peptide: Protein Rep68
    • Complex: AAV8 capsid
      • Protein or peptide: Capsid protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsAdeno-associated virus / AAV / AAA+ ATPase / VIRUS
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
Protein Rep68 / Capsid protein
Similarity search - Component
Biological speciesadeno-associated virus 8 / adeno-associated virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsRouse SL / Bubeck D / Barritt JD / Xu V / Wake M
Funding support2 items
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 JD / Bubeck D / Wake M / Rouse SL
History
DepositionJul 9, 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_54328.png

Downloads & links

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Map

FileDownload / File: emd_54328.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 540 pix.
= 502.74 Å		0.93 Å/pix.
x 540 pix.
= 502.74 Å		0.93 Å/pix.
x 540 pix.
= 502.74 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.931 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0397
Minimum - Maximum-0.12819658 - 0.3601025
Average (Standard dev.)0.00034945618 (±0.0061977594)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 502.74 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54328_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_54328_additional_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54328_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_54328_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Pentameric AAV2 Rep40 in complex with AAV8 capsid

EntireName: Pentameric AAV2 Rep40 in complex with AAV8 capsid
Components
  • Complex: Pentameric AAV2 Rep40 in complex with AAV8 capsid
    • Complex: Pentameric AAV2 Rep40
      • Protein or peptide: Protein Rep68
    • Complex: AAV8 capsid
      • Protein or peptide: Capsid protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Pentameric AAV2 Rep40 in complex with AAV8 capsid

SupramoleculeName: Pentameric AAV2 Rep40 in complex with AAV8 capsid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: From local refinement of 1/12 5-fold vertex of the Rep-bound AAV8 capsid
Source (natural)Organism: adeno-associated virus 8

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Supramolecule #2: Pentameric AAV2 Rep40

SupramoleculeName: Pentameric AAV2 Rep40 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: adeno-associated virus 2

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Supramolecule #3: AAV8 capsid

SupramoleculeName: AAV8 capsid / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: adeno-associated virus 2

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Details: WT AAV8 VP1/2/3 truncated to fit in map / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: adeno-associated virus 8
Molecular weightTheoretical: 81.833047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAADGYLPDW LEDNLSEGIR EWWALKPGAP KPKANQQKQD DGRGLVLPGY KYLGPFNGLD KGEPVNAADA AALEHDKAYD QQLQAGDNP YLRYNHADAE FQERLQEDTS FGGNLGRAVF QAKKRVLEPL GLVEEGAKTA PGKKRPVEPS PQRSPDSSTG I GKKGQQPA ...String:
MAADGYLPDW LEDNLSEGIR EWWALKPGAP KPKANQQKQD DGRGLVLPGY KYLGPFNGLD KGEPVNAADA AALEHDKAYD QQLQAGDNP YLRYNHADAE FQERLQEDTS FGGNLGRAVF QAKKRVLEPL GLVEEGAKTA PGKKRPVEPS PQRSPDSSTG I GKKGQQPA RKRLNFGQTG DSESVPDPQP LGEPPAAPSG VGPNTMAAGG GAPMADNNEG ADGVGSSSGN WHCDSTWLGD RV ITTSTRT WALPTYNNHL YKQISNGTSG GATNDNTYFG YSTPWGYFDF NRFHCHFSPR DWQRLINNNW GFRPKRLSFK LFN IQVKEV TQNEGTKTIA NNLTSTIQVF TDSEYQLPYV LGSAHQGCLP PFPADVFMIP QYGYLTLNNG SQAVGRSSFY CLEY FPSQM LRTGNNFQFT YTFEDVPFHS SYAHSQSLDR LMNPLIDQYL YYLSRTQTTG GTANTQTLGF SQGGPNTMAN QAKNW LPGP CYRQQRVSTT TGQNNNSNFA WTAGTKYHLN GRNSLANPGI AMATHKDDEE RFFPSNGILI FGKQNAARDN ADYSDV MLT SEEEIKTTNP VATEEYGIVA DNLQQQNTAP QIGTVNSQGA LPGMVWQNRD VYLQGPIWAK IPHTDGNFHP SPLMGGF GL KHPPPQILIK NTPVPADPPT TFNQSKLNSF ITQYSTGQVS VEIEWELQKE NSKRWNPEIQ YTSNYYKSTS VDFAVNTE G VYSEPRPIGT RYLTRNL

UniProtKB: Capsid protein

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Macromolecule #2: Protein Rep68

MacromoleculeName: Protein Rep68 / type: protein_or_peptide / ID: 2 / Details: Latch-WTAAV2Rep40-TrB-3xFLAG-TEV-6xHis / Number of copies: 5 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: adeno-associated virus 8
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 Rep68

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 12 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 10 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 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: 130000
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: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 191887
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 modelPDB ID:

6v12


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

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

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