[English] 日本語
Yorodumi
- EMDB-20624: Empty AAV3B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20624
TitleEmpty AAV3B
Map dataEmpty AAV3B (No genome)
SampleParvoviridae != Adeno-associated virus 3B

Parvoviridae

  • Virus: Adeno-associated virus 3B
    • Protein or peptide: AAV3B
Biological speciesHomo sapiens (human) / Adeno-associated virus 3B
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsSubramanian S / Hafenstein S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute1S10OD011986-01A1 United States
CitationJournal: Hum Gene Ther / Year: 2019
Title: Filling Adeno-Associated Virus Capsids: Estimating Success by Cryo-Electron Microscopy.
Authors: Suriyasri Subramanian / Anna C Maurer / Carol M Bator / Alexander M Makhov / James F Conway / Kevin B Turner / James H Marden / Luk H Vandenberghe / Susan L Hafenstein /
Abstract: Adeno-associated viruses (AAVs) have been employed successfully as gene therapy vectors in treating various genetic diseases for almost two decades. However, transgene packaging is usually imperfect, ...Adeno-associated viruses (AAVs) have been employed successfully as gene therapy vectors in treating various genetic diseases for almost two decades. However, transgene packaging is usually imperfect, and developing a rapid and accurate method for measuring the proportion of DNA encapsidation is an important step for improving the downstream process of large scale vector production. In this study, we used two-dimensional class averages and three-dimensional classes, intermediate outputs in the single particle cryo-electron microscopy (cryo-EM) image reconstruction pipeline, to determine the proportion of DNA-packaged and empty capsid populations. Two different preparations of AAV3 were analyzed to estimate the minimum number of particles required to be sampled by cryo-EM in order for robust calculation of the proportion of the full versus empty capsids in any given sample. Cost analysis applied to the minimum amount of data required for a valid ratio suggests that cryo-EM is an effective approach to analyze vector preparations.
History
DepositionAug 20, 2019-
Header (metadata) releaseSep 4, 2019-
Map releaseOct 2, 2019-
UpdateJan 1, 2020-
Current statusJan 1, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20624.png

Downloads & links

-
Map

FileDownload / File: emd_20624.map.gz / Format: CCP4 / Size: 193.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEmpty AAV3B (No genome)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 370 pix.
= 420.32 Å		1.14 Å/pix.
x 370 pix.
= 420.32 Å		1.14 Å/pix.
x 370 pix.
= 420.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.136 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.22815043 - 0.4075029
Average (Standard dev.)0.0009895375 (±0.023660861)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions370370370
Spacing370370370
CellA=B=C: 420.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1361.1361.136
M x/y/z370370370
origin x/y/z0.0000.0000.000
length x/y/z420.320420.320420.320
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ720720720
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS370370370
D min/max/mean-0.2280.4080.001

-
Supplemental data

-
Sample components

-
Entire : Parvoviridae

EntireName: Parvoviridae (virus)
Components
  • Virus: Adeno-associated virus 3B
    • Protein or peptide: AAV3B

-
Supramolecule #1: Adeno-associated virus 3B

SupramoleculeName: Adeno-associated virus 3B / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 68742 / Sci species name: Adeno-associated virus 3B / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Mus spretus (western wild mouse)
Host systemOrganism: Homo sapiens (human) / Recombinant cell: HEK
Virus shellShell ID: 1 / Diameter: 250.0 Å / T number (triangulation number): 1

-
Macromolecule #1: AAV3B

MacromoleculeName: AAV3B / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAADGYLPDW LEDNLSEGIR EWWALKPGVP QPKANQQHQD NRRGLVLPGY KYLGPGNGLD KGEPVNEAD AAALEHDKAY DQQLKAGDNP YLKYNHADAE FQERLQEDTS FGGNLGRAVF Q AKKRILEP LGLVEEAAKT APGKKRPVDQ SPQEPDSSSG VGKSGKQPAR ...String:
MAADGYLPDW LEDNLSEGIR EWWALKPGVP QPKANQQHQD NRRGLVLPGY KYLGPGNGLD KGEPVNEAD AAALEHDKAY DQQLKAGDNP YLKYNHADAE FQERLQEDTS FGGNLGRAVF Q AKKRILEP LGLVEEAAKT APGKKRPVDQ SPQEPDSSSG VGKSGKQPAR KRLNFGQTGD SE SVPDPQP LGEPPAAPTS LGSNTMASGG GAPMADNNEG ADGVGNSSGN WHCDSQWLGD RVI TTSTRT WALPTYNNHL YKQISSQSGA SNDNHYFGYS TPWGYFDFNR FHCHFSPRDW QRLI NNNWG FRPKKLSFKL FNIQVKEVTQ NDGTTTIANN LTSTVQVFTD SEYQLPYVLG SAHQG CLPP FPADVFMVPQ YGYLTLNNGS QAVGRSSFYC LEYFPSQMLR TGNNFQFSYT FEDVPF HSS YAHSQSLDRL MNPLIDQYLY YLNRTQGTTS GTTNQSRLLF SQAGPQSMSL QARNWLP GP CYRQQRLSKT ANDNNNSNFP WTAASKYHLN GRDSLVNPGP AMASHKDDEE KFFPMHGN L IFGKEGTTAS NAELDNVMIT DEEEIRTTNP VATEQYGTVA NNLQSSNTAP TTRTVNDQG ALPGMVWQDR DVYLQGPIWA KIPHTDGHFH PSPLMGGFGL KHPPPQIMIK NTPVPANPPT TFSPAKFAS FITQYSTGQV SVEIEWELQK ENSKRWNPEI QYTSNYNKSV NVDFTVDTNG V YSEPRPIG TRYLTRNL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClsodium chloride
1.7 mMKClpotassium chloride
10.0 mMNa2HPO4sodium phosphate dibasic
1.8 mMKH2PO4potassium phosphate monobasic

Details: Phosphate buffered saline pH 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 2082 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
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: 132631
Details: Manual picking was used to handpick 1000 particles which were used as template to then autopick
CTF correctionSoftware - Name: Gctf
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 22096
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
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