[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

TitleCryo-EM elucidates the interaction mechanism of ozoralizumab, a humanized anti-TNFα NANOBODY® compound.
Journal, issue, pagesBiochem Biophys Res Commun, Vol. 816, Page 153572, Year 2026
Publish dateJun 4, 2026
AuthorsMasashi Mima / Kyohei Sato / Takeshi Yokoyama / Chiemi Mishima-Tsumagari / Tatsuya Ohnuki / Yoshikazu Tanaka / Kunihiko Iwamoto /
PubMed AbstractOzoralizumab (OZR) is a next-generation TNF inhibitor composed of two identical humanized anti-TNFα NANOBODY® molecules (TNF30s) recombinantly linked via one humanized anti-human serum albumin (HSA) ...Ozoralizumab (OZR) is a next-generation TNF inhibitor composed of two identical humanized anti-TNFα NANOBODY® molecules (TNF30s) recombinantly linked via one humanized anti-human serum albumin (HSA) NANOBODY® molecule (ALB8) and two peptide linkers. OZR is designed as a unique format to exert potent inhibitory effects against TNFα with long plasma half-life. However, the three-dimensional structure of OZR-TNFα-HSA complex has not yet been elucidated, and a complete understanding of its interaction mechanism with TNFα is yet to be gained. In this study, we successfully observed the formation of the OZR-TNFα-HSA ternary complex by single-particle cryo-electron microscopy. The single-particle analysis revealed that the two TNF30 molecules of OZR simultaneously bind bivalently to TNFα in a 1:1-bivalent binding mode, while the ALB8 molecule binds to HSA, forming a ternary complex. Thus, OZR exhibits a binding mode significantly different from that of other IgG-type TNFα inhibitors. Furthermore, surface plasmon resonance (SPR) analysis demonstrated that the 1:1-bivalent binding mode confers an exceptionally slow dissociation rate, thereby contributing to the potent TNFα-neutralizing activity of OZR. These findings not only lend support to the favorable clinical efficacy of OZR from a structural standpoint but also lay the foundation for the rational design and development of next-generation TNFα inhibitors with enhanced and sustained efficacy.
External linksBiochem Biophys Res Commun / PubMed:41935434
MethodsEM (single particle)
Resolution2.43 - 6.19 Å
Structure data

67993

21tv

EMDB-67993, PDB-21tv:
Cryo-EM structure of the TNF-alpha-Ozoralizumab (OZR)-HSA complex
Method: EM (single particle) / Resolution: 6.19 Å

67994

21tw

EMDB-67994: TNF-alpha in complex with the TNF-alpha inhibitor Ozoralizumab (OZR)
PDB-21tw: Cryo-EM structure of TNF-alpha in complex with two anti-TNF-alpha nanobodies, TNF30, derived from the TNF-alpha inhibitor Ozoralizumab (OZR)
Method: EM (single particle) / Resolution: 2.43 Å

Source
  • homo sapiens (human)
KeywordsCYTOKINE / NANOBODY / VHH / TNF-alpha / HSA / Ozoralizumab / OZR

+
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