[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructural basis of liver de-targeting and neuronal tropism of CNS-targeted AAV capsids.
Journal, issue, pagesMol Ther, Year 2026
Publish dateMar 28, 2026
AuthorsTyler J Brittain / Seongmin Jang / Gerard M Coughlin / Jonathan D Hoang / Bre'Anna H Barcelona / Izabela Giriat / Fiona Ristic / Nathan Appling / Camille P M A Chossis / Timothy F Shay / Viviana Gradinaru /
PubMed AbstractDeveloping effective vectors for gene therapy requires accurate on-target coverage while minimizing off-target transduction that can lead to adverse events. In mice, the engineered capsid PHP.eB ...Developing effective vectors for gene therapy requires accurate on-target coverage while minimizing off-target transduction that can lead to adverse events. In mice, the engineered capsid PHP.eB shows enhanced brain transduction, while the further engineered CAP-B10 is also de-targeted from astrocytes and liver. Here, we solved cryoelectron microscopy (cryo-EM) structures of CAP-B10 and its complex with the adeno-associated virus receptor (AAVR) domain PKD2, at 2.22- and 2.20-Å resolutions, respectively. These structures reveal a motif that hinders AAVR binding, which we confirmed by measuring affinities. We showed that this motif is transferable to other capsids by solving cryo-EM structures of AAV9-X1, at 3.09 Å, and AAV9-X1.1 without and with PKD2, at 2.51 and 2.18 Å, respectively. Using this structural information, we designed and validated novel AAV variants with reduced liver and altered brain cell tropism in vivo. Overall, we provide a framework for using structural information to guide rational engineering of gene delivery vectors to achieve safe and effective delivery.
External linksMol Ther / PubMed:41906393
MethodsEM (single particle)
Resolution2.05 - 3.09 Å
Structure data

71273

9p4l

EMDB-71273, PDB-9p4l:
Cryo-EM structure of AAV.CAP-B10
Method: EM (single particle) / Resolution: 2.22 Å

71274

9p4m

EMDB-71274, PDB-9p4m:
Cryo-EM structure of AAV9-B10
Method: EM (single particle) / Resolution: 3.05 Å

71275

9p4n

EMDB-71275, PDB-9p4n:
Cryo-EM structure of AAV9-X1.1 complexed to AAVR-PKD2
Method: EM (single particle) / Resolution: 2.18 Å

71276

9p4o

EMDB-71276, PDB-9p4o:
Cryo-EM structure of PHP.eB.24
Method: EM (single particle) / Resolution: 2.05 Å

71277

9p4p

EMDB-71277, PDB-9p4p:
Cryo-EM structure of AAV9-X1
Method: EM (single particle) / Resolution: 3.09 Å

71278

9p4q

EMDB-71278, PDB-9p4q:
Cryo-EM structure of AAV.CAP-B10 complexed to AAVR-PKD2
Method: EM (single particle) / Resolution: 2.2 Å

71279

9p4r

EMDB-71279, PDB-9p4r:
Cryo-EM structure of AAV9-X1.1
Method: EM (single particle) / Resolution: 2.51 Å

Source
  • adeno-associated virus
  • mus musculus (house mouse)
KeywordsVIRUS / AAV / liver / detarget / PHP.eB / CAP-B10 / AAV9 / AAV9-X1.1 / X1.1 / LRP6 / AAVR / PKD2 / X1 / receptor / complex / liver detarget

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more