[English] 日本語
Yorodumi
- EMDB-20693: Adeno-associated virus strain AAVhu.37 capsid icosahedral structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20693
TitleAdeno-associated virus strain AAVhu.37 capsid icosahedral structure
Map dataicosahedrally-averaged map of AAVhu.37
Sample
  • Virus: Adeno-associated virus
    • Protein or peptide: Capsid protein VP1
Keywordscapsid / blood-brain barrier penetration / VIRUS
Function / homologyPhospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / Capsid protein VP1
Function and homology information
Biological speciesAdeno-associated virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsKaelber JT / Yost SA
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2020
Title: Structure of the AAVhu.37 capsid by cryoelectron microscopy.
Authors: Jason T Kaelber / Samantha A Yost / Keith A Webber / Emre Firlar / Ye Liu / Olivier Danos / Andrew C Mercer /
Abstract: Adeno-associated viruses (AAVs) are used as in vivo gene-delivery vectors in gene-therapy products and have been heavily investigated for numerous indications. Over 100 naturally occurring AAV ...Adeno-associated viruses (AAVs) are used as in vivo gene-delivery vectors in gene-therapy products and have been heavily investigated for numerous indications. Over 100 naturally occurring AAV serotypes and variants have been isolated from primate samples. Many reports have described unique properties of these variants (for instance, differences in potency, target cell or evasion of the immune response), despite high amino-acid sequence conservation. AAVhu.37 is of interest for clinical applications owing to its proficient transduction of the liver and central nervous system. The sequence identity of the AAVhu.37 VP1 to the well characterized AAVrh.10 serotype, for which no structure is available, is greater than 98%. Here, the structure of the AAVhu.37 capsid at 2.56 Å resolution obtained via single-particle cryo-electron microscopy is presented.
History
DepositionSep 6, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseSep 18, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.75
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.75
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6u95
  • Surface level: 0.75
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6u95
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20693.png

Downloads & links

-
Map

FileDownload / File: emd_20693.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationicosahedrally-averaged map of AAVhu.37
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 560 pix.
= 392.364 Å		0.7 Å/pix.
x 560 pix.
= 392.364 Å		0.7 Å/pix.
x 560 pix.
= 392.364 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.70065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.75 / Movie #1: 0.75
Minimum - Maximum-0.7067622 - 1.3878311
Average (Standard dev.)0.043222647 (±0.2187148)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-280-280-280
Dimensions560560560
Spacing560560560
CellA=B=C: 392.36398 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.700650.700650.70065
M x/y/z560560560
origin x/y/z0.0000.0000.000
length x/y/z392.364392.364392.364
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ254265109
MAP C/R/S123
start NC/NR/NS-280-280-280
NC/NR/NS560560560
D min/max/mean-0.7071.3880.043

-
Supplemental data

-
Half map: half A

Fileemd_20693_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half B

Fileemd_20693_half_map_2.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Adeno-associated virus

EntireName: Adeno-associated virus
Components
  • Virus: Adeno-associated virus
    • Protein or peptide: Capsid protein VP1

-
Supramolecule #1: Adeno-associated virus

SupramoleculeName: Adeno-associated virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Virions containing GFP-encoding ssDNA were assembled in transfected HEK293T helper cells.
NCBI-ID: 272636 / Sci species name: Adeno-associated virus / Sci species strain: hu.37 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5 MDa
Virus shellShell ID: 1 / Diameter: 250.0 Å / T number (triangulation number): 1

-
Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus
Molecular weightTheoretical: 81.528852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AADGYLPDWL EDNLSEGIRE WWDLKPGAPK PKANQQKQDD GRGLVLPGYK YLGPFNGLDK GEPVNAADAA ALEHDKAYDQ QLKAGDNPY LRYNHADAEF QERLQEDTSF GGNLGRAVFQ AKKRVLEPLG LVEEAAKTAP GKKRPVEPSP QRSPDSSTGI G KKGQQPAK ...String:
AADGYLPDWL EDNLSEGIRE WWDLKPGAPK PKANQQKQDD GRGLVLPGYK YLGPFNGLDK GEPVNAADAA ALEHDKAYDQ QLKAGDNPY LRYNHADAEF QERLQEDTSF GGNLGRAVFQ AKKRVLEPLG LVEEAAKTAP GKKRPVEPSP QRSPDSSTGI G KKGQQPAK KRLNFGQTGD SESVPDPQPI GEPPAGPSGL GSGTMAAGGG APMADNNEGA DGVGSSSGNW HCDSTWLGDR VI TTSTRTW ALPTYNNHLY KQISNGTSGG STNDNTYFGY STPWGYFDFN RFHCHFSPRD WQRLINNNWG FRPKRLSFKL FNI QVKEVT QNEGTKTIAN NLTSTIQVFT DSEYQLPYVL GSAHQGCLPP FPADVFMIPQ YGYLTLNNGS QAVGRSSFYC LEYF PSQML RTGNNFEFSY TFEDVPFHSS YAHSQSLDRL MNPLIDQYLY YLSRTQSTGG TQGTQQLLFS QAGPANMSAQ AKNWL PGPC YRQQRVSTTL SQNNNSNFAW TGATKYHLNG RDSLVNPGVA MATHKDDEER FFPSSGVLMF GKQGAGRDNV DYSSVM LTS EEEIKTTNPV ATEQYGVVAD NLQQTNTGPI VGNVNSQGAL PGMVWQNRDV YLQGPIWAKI PHTDGNFHPS PLMGGFG LK HPPPQILIKN TPVPADPPTT FSQAKLASFI TQYSTGQVSV EIEWELQKEN SKRWNPEIQY TSNYYKSTNV DFAVNTEG T YSEPRPIGTR YLTRNL

UniProtKB: Capsid protein VP1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
9.0 g/LNaClsodium chloride
0.144 g/LKH2PO4potassium phosphate dibasic
0.795 g/LNa2HPO4sodium phosphate monobasic

Details: PBS
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.86 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.037 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: LEICA EM GP
Details: Whatman #1 filter paper, 4.5s blot. 3.5 microliters specimen applied..
Detailsapprox. 7*10^13 genome copies per mL

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsChromatic aberration corrector: none / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-25 / Number grids imaged: 1 / Average exposure time: 5.0 sec. / Average electron dose: 1.31 e/Å2 / Details: collected in superresolution mode
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 1.584 µm / Calibrated defocus min: 0.535 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 53545
Startup modelType of model: NONE / Details: ab initio
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.9.0)
Details: 2.8 unmasked, 2.53 masked, 2.56 with noise-substitution ("true FSC"). 2.7 3-bit unmasked.
Number images used: 41850
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.9.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.9.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.9.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

2qa0


Chain - Chain ID: A / Chain - Residue range: 220-738 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6u95:
Adeno-associated virus strain AAVhu.37 capsid icosahedral structure

+
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