[English] 日本語
Yorodumi
- EMDB-79003: AAV2 Rep68(delta1-209)/capsid/DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-79003
TitleAAV2 Rep68(delta1-209)/capsid/DNA complex
Map dataReconstruction of non-subtracted particles with orientations/positions mapped back from the Additional Map
Sample
  • Virus: adeno-associated virus 2
    • Protein or peptide: Protein Rep68
    • Protein or peptide: Capsid protein VP1
  • DNA: ssDNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PYROPHOSPHATE 2-
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Keywordsvirion / replicase / 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 / 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
Protein Rep68 / Capsid protein VP1
Similarity search - Component
Biological speciesAdeno-associated virus 2 Srivastava/1982 / synthetic construct (others) / adeno-associated virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsKaelber JT / Barnakov V / Shen J / Escalante CR
Funding support United States, 2 items
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 JT / Barnakov V / Shen J / Hernandez K / Tarbox HJ / Khan A / Escalante CR
History
DepositionSep 9, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_79003.png

Downloads & links

-
Map

FileDownload / File: emd_79003.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of non-subtracted particles with orientations/positions mapped back from the Additional Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 756 pix.
= 487.62 Å		0.65 Å/pix.
x 756 pix.
= 487.62 Å		0.65 Å/pix.
x 756 pix.
= 487.62 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.645 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.2775766 - 0.5466949
Average (Standard dev.)0.002816866 (±0.029602163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions756756756
Spacing756756756
CellA=B=C: 487.62 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_79003_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Reconstruction of capsid-subtracted particles showing higher resolution in...

Fileemd_79003_additional_1.map
AnnotationReconstruction of capsid-subtracted particles showing higher resolution in the rep/DNA region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_79003_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_79003_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : adeno-associated virus 2

EntireName: adeno-associated virus 2
Components
  • Virus: adeno-associated virus 2
    • Protein or peptide: Protein Rep68
    • Protein or peptide: Capsid protein VP1
  • DNA: ssDNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PYROPHOSPHATE 2-
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

-
Supramolecule #1: adeno-associated virus 2

SupramoleculeName: adeno-associated virus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1, #3 / NCBI-ID: 10804 / Sci species name: adeno-associated virus 2 / Sci species strain: Srivastava/1982 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.2 MDa
Virus shellShell ID: 1 / Diameter: 280.0 Å / T number (triangulation number): 1

-
Macromolecule #1: Protein Rep68

MacromoleculeName: Protein Rep68 / type: protein_or_peptide / ID: 1
Details: Deletion construct lacking residues 1-209 from AAV2 rep68
Number of copies: 6 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Adeno-associated virus 2 Srivastava/1982
Molecular weightTheoretical: 31.403645 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: APVIRSKTSA RYMELVGWLV DKGITSEKQW IQEDQASYIS FNAASNSRSQ IKAALDNAGK IMSLTKTAPD YLVGQQPVED ISSNRIYKI LELNGYDPQY AASVFLGWAT KKFGKRNTIW LFGPATTGKT NIAEAIAHTV PFYGCVNWTN ENFPFNDCVD K MVIWWEEG ...String:
APVIRSKTSA RYMELVGWLV DKGITSEKQW IQEDQASYIS FNAASNSRSQ IKAALDNAGK IMSLTKTAPD YLVGQQPVED ISSNRIYKI LELNGYDPQY AASVFLGWAT KKFGKRNTIW LFGPATTGKT NIAEAIAHTV PFYGCVNWTN ENFPFNDCVD K MVIWWEEG KMTAKVVESA KAILGGSKVR VDQKCKSSAQ IDPTPVIVTS NTNMCAVIDG NSTTFEHQQP LQDRMFKFEL TR RLDHDFG KVTKQEVKDF FRWAKDHVVE VEHEFYVKKG G

UniProtKB: Protein Rep68

-
Macromolecule #3: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus 2 Srivastava/1982
Molecular weightTheoretical: 58.027895 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GNWHCDSTWM GDRVITTSTR TWALPTYNNH LYKQISSQSG ASNDNHYFGY STPWGYFDFN RFHCHFSPRD WQRLINNNWG FRPKRLNFK LFNIQVKEVT QNDGTTTIAN NLTSTVQVFT DSEYQLPYVL GSAHQGCLPP FPADVFMVPQ YGYLTLNNGS Q AVGRSSFY ...String:
GNWHCDSTWM GDRVITTSTR TWALPTYNNH LYKQISSQSG ASNDNHYFGY STPWGYFDFN RFHCHFSPRD WQRLINNNWG FRPKRLNFK LFNIQVKEVT QNDGTTTIAN NLTSTVQVFT DSEYQLPYVL GSAHQGCLPP FPADVFMVPQ YGYLTLNNGS Q AVGRSSFY CLEYFPSQML RTGNNFTFSY TFEDVPFHSS YAHSQSLDRL MNPLIDQYLY YLSRTNTPSG TTTQSRLQFS QA GASDIRD QSRNWLPGPC YRQQRVSKTS ADNNNSEYSW TGATKYHLNG RDSLVNPGPA MASHKDDEEK FFPQSGVLIF GKQ GSEKTN VDIEKVMITD EEEIRTTNPV ATEQYGSVST NLQRGNRQAA TADVNTQGVL PGMVWQDRDV YLQGPIWAKI PHTD GHFHP SPLMGGFGLK HPPPQILIKN TPVPANPSTT FSAAKFASFI TQYSTGQVSV EIEWELQKEN SKRWNPEIQY TSNYN KSVN VDFTVDTNGV YSEPRPIGTR YLTRNL

UniProtKB: Capsid protein VP1

-
Macromolecule #2: ssDNA

MacromoleculeName: ssDNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.215713 KDa
SequenceString:
(DN)(DN)(DN)(DN)(DN)(DN)(DN)

-
Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 8 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

-
Macromolecule #5: PYROPHOSPHATE 2-

MacromoleculeName: PYROPHOSPHATE 2- / type: ligand / ID: 5 / Number of copies: 1 / Formula: POP
Molecular weightTheoretical: 175.959 Da
Chemical component information

ChemComp-POP:
PYROPHOSPHATE 2-

-
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 10 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #7: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 7 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride
10.0 mMNa2HPO4sodium phosphate dibasic
1.8 mMKH2PO4potassium phosphate monobasic
5.0 mMMgCl2magnesium chloride
5.0 mMC10H12N5O12P3SATPgammaS

Details: PBS plus ATPgammaS and MgCl2
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 21603 / Average electron dose: 64.96 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 73031
Details: template picking of icosahedral particles, before symmetry expansion
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: 3D reconstruction of similar map, undeposited
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Details: symmetry-expanded particles post-classification / Number images used: 249955
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 28 / Avg.num./class: 92895 / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

12kg
PDB Unreleased entry


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

+
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