[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 requirements of blood factors binding to soluble hexon trimers with implications for adenovirus cell targeting and immune evasion.
Journal, issue, pagesPLoS Pathog, Vol. 22, Issue 7, Page e1014389, Year 2026
Publish dateJul 13, 2026
AuthorsOlivia X Ma / Shao-Chia Lu / Haley E Mudrick / Mary E Barry / Jarrod B French / Michael A Barry / Vijay S Reddy /
PubMed AbstractHuman adenovirus serotype 5 (HAdV-C5) is widely used as a gene delivery vector in both experimental and clinical settings. Upon intravenous administration, HAdV-C5 exhibits strong liver tropism, ...Human adenovirus serotype 5 (HAdV-C5) is widely used as a gene delivery vector in both experimental and clinical settings. Upon intravenous administration, HAdV-C5 exhibits strong liver tropism, largely mediated by interactions between its major capsid protein, hexon (Hx), and coagulation factor X (FX). In contrast, the closely related species C adenovirus 6 (HAdV-C6) also targets the liver but shows reduced dependency on coagulation factors, whereas species D adenovirus 26 (HAdV-D26) does not bind coagulation factors altogether. To define the structural basis of this serotype-specific host factor recognition, we determined high-resolution cryo-electron microscopy structures of isolated hexon trimers from HAdV-C5 and HAdV-C6 in complex with coagulation factors FX and prothrombin (factor II, FII). The resulting atomic models reveal conserved binding interfaces involving the γ-carboxyglutamic acid (Gla) domains of both coagulation factors and the hypervariable regions HVR5 and HVR7 lining the surface cavities of HAdV-C5 and HAdV-C6 hexons. Structures of hexon complexes formed by co-incubation with both FX and FII further reveal serotype-specific binding preferences under physiologically relevant conditions, showing that HAdV-C5 hexon preferentially engages FX, whereas HAdV-C6 hexon favors FII. By contrast, HAdV-D26 hexon does not bind either factor, likely due to an insertion constrained by proline residues in the HVR5 loop that restricts the factor access to the hexon cavity. Together, these findings provide a detailed structural framework for adenovirus-coagulation factor interactions and support the rational engineering of adenovirus vectors with improved targeting and safety profiles.
External linksPLoS Pathog / PubMed:42441716 / PubMed Central
MethodsEM (single particle)
Resolution3.17 - 3.26 Å
Structure data

EMDB-76963, PDB-13cm:
HAdV-C5 Hexon with coagulation factor II
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-76991, PDB-13dj:
HAdV-C5 hexon trimer
Method: EM (single particle) / Resolution: 3.17 Å

EMDB-76994, PDB-13dm:
HAdV-C6 Hexon trimer
Method: EM (single particle) / Resolution: 3.26 Å

EMDB-77024, PDB-13er:
Cryo-EM structure of HAdV-C6 hexon trimer in complex with prothrombin (FII)
Method: EM (single particle) / Resolution: 3.22 Å

EMDB-77025, PDB-13es:
Cryo-EM structure of HAdV-C5 hexon trimer in complex with human coagulation factor X (FX)
Method: EM (single particle) / Resolution: 3.23 Å

EMDB-77027, PDB-13eu:
Cryo-EM structure of HAdV-C6 hexon trimer in complex with human coagulation factor X (FX)
Method: EM (single particle) / Resolution: 3.26 Å

Chemicals

ChemComp-CA:
Unknown entry

Source
  • human adenovirus 5
  • homo sapiens (human)
  • human adenovirus 6
KeywordsVIRAL PROTEIN / adenovirus / hexon / coagulation factor II / virus-host interaction / cryo-EM / virus capsid / HAdV-C5 / coagulation factor X

+
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