[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

TitleModulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies.
Journal, issue, pagesCell, Year 2024
Publish dateJun 7, 2024
AuthorsNatasha I Edman / Ashish Phal / Rachel L Redler / Thomas Schlichthaerle / Sanjay R Srivatsan / Devon Duron Ehnes / Ali Etemadi / Seong J An / Andrew Favor / Zhe Li / Florian Praetorius / Max Gordon / Thomas Vincent / Silvia Marchiano / Leslie Blakely / Chuwei Lin / Wei Yang / Brian Coventry / Derrick R Hicks / Longxing Cao / Neville Bethel / Piper Heine / Analisa Murray / Stacey Gerben / Lauren Carter / Marcos Miranda / Babak Negahdari / Sangwon Lee / Cole Trapnell / Ying Zheng / Charles E Murry / Devin K Schweppe / Benjamin S Freedman / Lance Stewart / Damian C Ekiert / Joseph Schlessinger / Jay Shendure / Gira Bhabha / Hannele Ruohola-Baker / David Baker /
PubMed AbstractMany growth factors and cytokines signal by binding to the extracellular domains of their receptors and driving association and transphosphorylation of the receptor intracellular tyrosine kinase ...Many growth factors and cytokines signal by binding to the extracellular domains of their receptors and driving association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affect signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo-designed fibroblast growth factor receptor (FGFR)-binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca release and mitogen-activated protein kinase (MAPK) pathway activation. The high specificity of the designed agonists reveals distinct roles for two FGFR splice variants in driving arterial endothelium and perivascular cell fates during early vascular development. Our designed modular assemblies should be broadly useful for unraveling the complexities of signaling in key developmental transitions and for developing future therapeutic applications.
External linksCell / PubMed:38861993
MethodsEM (single particle)
Resolution4.0 - 13.0 Å
Structure data

28889

8f6r

EMDB-28889, PDB-8f6r:
CryoEM structure of designed modular protein oligomer C6-79
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-28958: CryoEM structure of designed modular protein oligomer C4-131
Method: EM (single particle) / Resolution: 9.1 Å

EMDB-28966: CryoEM map of de novo designed oligomeric protein C4-71_6x
Method: EM (single particle) / Resolution: 9.0 Å

EMDB-28967: CryoEM map of de novo designed oligomeric protein C4-71_8x
Method: EM (single particle) / Resolution: 13.0 Å

EMDB-28968: CryoEM map of de novo designed oligomeric protein C6-71
Method: EM (single particle) / Resolution: 9.0 Å

EMDB-28969: CryoEM map of de novo designed oligomeric protein C6-71_6x
Method: EM (single particle) / Resolution: 8.0 Å

EMDB-28970: CryoEM map of de novo designed oligomeric protein C6-71_8x
Method: EM (single particle) / Resolution: 6.0 Å

EMDB-28971: CryoEM map of de novo designed oligomeric protein C8-71_6x
Method: EM (single particle) / Resolution: 7.0 Å

EMDB-28972: CryoEM map of de novo designed oligomeric protein C8-71_8x
Method: EM (single particle) / Resolution: 7.0 Å

EMDB-28973: CryoEM map of de novo designed oligomeric protein C4-81
Method: EM (single particle) / Resolution: 5.4 Å

EMDB-28974: CryoEM map of designed oligomeric protein C4-71
Method: EM (single particle) / Resolution: 5.1 Å

Source
  • synthetic construct (others)
KeywordsDE NOVO PROTEIN / Synthetic / Self-assembling / Oligomeric / Helical repeats

+
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://pdbjlvh1.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