[English] 日本語
Yorodumi
- EMDB-54184: Heptameric AAV2 Rep40-dsDNA (ITR) complex in presence of ATPgS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54184
TitleHeptameric AAV2 Rep40-dsDNA (ITR) complex in presence of ATPgS
Map data
Sample
  • Complex: AAV2 Heptameric Rep40-dsDNA (ITR) in presence of ATPgS
    • DNA: DNA (28-MER)
    • Protein or peptide: Protein Rep40
  • 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 / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 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 26, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54184.png

Downloads & links

-
Map

FileDownload / File: emd_54184.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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: 4.87
Minimum - Maximum-22.697766999999999 - 59.453360000000004
Average (Standard dev.)0.013850825 (±1.1671793)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Sample components

-
Entire : AAV2 Heptameric Rep40-dsDNA (ITR) in presence of ATPgS

EntireName: AAV2 Heptameric Rep40-dsDNA (ITR) in presence of ATPgS
Components
  • Complex: AAV2 Heptameric Rep40-dsDNA (ITR) in presence of ATPgS
    • DNA: DNA (28-MER)
    • Protein or peptide: Protein Rep40
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: AAV2 Heptameric Rep40-dsDNA (ITR) in presence of ATPgS

SupramoleculeName: AAV2 Heptameric Rep40-dsDNA (ITR) 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 DNA and ATP-gamma-S
Source (natural)Organism: adeno-associated virus 2

-
Macromolecule #1: DNA (28-MER)

MacromoleculeName: DNA (28-MER) / type: dna / ID: 1
Details: dsDNA segment from full length AAV2 5' Inverted Terminal Repeat hairpin DNA: (5'->3') ...Details: dsDNA segment from full length AAV2 5' Inverted Terminal Repeat hairpin DNA: (5'->3') TTGGCCACTCCCTCTCTGCGCGCTCGCTCGCTCACTGAGGCCGGGCGACCAAAGGTCGCCCGACGCCCGGGCTTTGCCCGGGCGGCCTCAGTGAGCGAGCGAGCGCGCAGAGAGGGAGTGGCCAACTCCATCACTAGGGGTTCCT
Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 44.697359 KDa
SequenceString: (DT)(DT)(DG)(DG)(DC)(DC)(DA)(DC)(DT)(DC) (DC)(DC)(DT)(DC)(DT)(DC)(DT)(DG)(DC)(DG) (DC)(DG)(DC)(DT)(DC)(DG)(DC)(DT)(DC) (DG)(DC)(DT)(DC)(DA)(DC)(DT)(DG)(DA)(DG) (DG) (DC)(DC)(DG)(DG)(DG)(DC) ...String:
(DT)(DT)(DG)(DG)(DC)(DC)(DA)(DC)(DT)(DC) (DC)(DC)(DT)(DC)(DT)(DC)(DT)(DG)(DC)(DG) (DC)(DG)(DC)(DT)(DC)(DG)(DC)(DT)(DC) (DG)(DC)(DT)(DC)(DA)(DC)(DT)(DG)(DA)(DG) (DG) (DC)(DC)(DG)(DG)(DG)(DC)(DG)(DA) (DC)(DC)(DA)(DA)(DA)(DG)(DG)(DT)(DC)(DG) (DC)(DC) (DC)(DG)(DA)(DC)(DG)(DC)(DC) (DC)(DG)(DG)(DG)(DC)(DT)(DT)(DT)(DG)(DC) (DC)(DC)(DG) (DG)(DG)(DC)(DG)(DG)(DC) (DC)(DT)(DC)(DA)(DG)(DT)(DG)(DA)(DG)(DC) (DG)(DA)(DG)(DC) (DG)(DA)(DG)(DC)(DG) (DC)(DG)(DC)(DA)(DG)(DA)(DG)(DA)(DG)(DG) (DG)(DA)(DG)(DT)(DG) (DG)(DC)(DC)(DA) (DA)(DC)(DT)(DC)(DC)(DA)(DT)(DC)(DA)(DC) (DT)(DA)(DG)(DG)(DG)(DG) (DT)(DT)(DC) (DC)(DT)

-
Macromolecule #2: Protein Rep40

MacromoleculeName: Protein Rep40 / type: protein_or_peptide / ID: 2 / Details: Latch-WTAAV2Rep40-TrB-3xFLAG-TEV-6xHis / Number of copies: 7 / 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

-
Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

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

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

-
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

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1)
Details: Composite map generated in phenix using 2 local maps (3-mer local map and 4-mer local map).
Number images used: 137594
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)

-
Atomic model buiding 1

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

PDB-9rqt:
Heptameric AAV2 Rep40-dsDNA (ITR) complex in presence of ATPgS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more