[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 for the differential recognition of integrin αvβ3 by rhodostomin and trimucrin.
Journal, issue, pagesCommun Biol, Vol. 9, Issue 1, Year 2026
Publish dateApr 27, 2026
AuthorsYa-Ting Wang / Yao-Tsung Chang / Chun-Hao Huang / Ching-Ting Liau / Chiu-Yueh Chen / Woei-Jer Chuang /
PubMed AbstractRhodostomin (Rho) and Trimucrin (Tmu) are RGD-containing disintegrins that inhibit integrins more effectively than short RGD peptides. They differ in their linker, RGD loop, and C-terminal sequences. ...Rhodostomin (Rho) and Trimucrin (Tmu) are RGD-containing disintegrins that inhibit integrins more effectively than short RGD peptides. They differ in their linker, RGD loop, and C-terminal sequences. We determined the X-ray structure of Tmu and the cryo-EM structures of integrin αvβ3 in complex with both disintegrins. Structural analysis revealed subtle differences in binding, with both adopting a rigid backbone conformation and interacting with integrin through three cooperative binding sites. Besides the conserved RGD interface, Tmu features a cluster of basic residues in its linker, while Rho has distinct C-terminal interactions. Disintegrin binding stabilizes αvβ3 in an extended-open conformation, while the β3-Y110 residue is essential for maintaining the bent state without ligands. These findings enhance our understanding of integrin recognition and inform the development of integrin-targeted therapeutics for anti-angiogenic, anti-tumor, and anti-inflammatory applications.
External linksCommun Biol / PubMed:42045602 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.68 - 2.79 Å
Structure data

60907

9iuj

EMDB-60907, PDB-9iuj:
Integrin alpha-v beta-3 in complex with rhodostomin
Method: EM (single particle) / Resolution: 2.78 Å

63364

9lt3

EMDB-63364, PDB-9lt3:
Integrin alpha-v beta-3 in complex with Trimucrin
Method: EM (single particle) / Resolution: 2.79 Å

PDB-9ual:
Crystal structure of Trimucrin
Method: X-RAY DIFFRACTION / Resolution: 1.68 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-ACT:
ACETATE ION

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
  • calloselasma rhodostoma (Malayan pit viper)
  • protobothrops mucrosquamatus (brown spotted pit viper)
KeywordsMEMBRANE PROTEIN / disintegrin / complex / BLOOD CLOTTING / Platelet aggregation inhibitor

+
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