[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

TitleMolecular basis of mitogen-activated protein kinase ERK2 activation by its upstream kinase MEK1.
Journal, issue, pagesbioRxiv, Year 2026
Publish dateJan 19, 2026
AuthorsJill von Velsen / Pauline Juyoux / Nicola Piasentin / Hayden Fisher / Karine Lapouge / Oscar Vadas / Francesco Luigi Gervasio / Matthew W Bowler /
PubMed AbstractThe RAS-RAF-MEK-ERK mitogen-activated protein kinase (MAPK) pathway relays extracellular signals into a cellular response and its dysregulation leads to many pathologies, particularly cancer. Here, ...The RAS-RAF-MEK-ERK mitogen-activated protein kinase (MAPK) pathway relays extracellular signals into a cellular response and its dysregulation leads to many pathologies, particularly cancer. Here, we determined cryo-EM structures of the MAP2K MEK1 activating its substrate MAPK ERK2, the final event in the cascade. We define the molecular details of specificity and phosphoryl transfer to the tyrosine of the ERK2 activation loop and examine the mechanism of substrate recognition using solution techniques and molecular dynamics. Binding of the substrate MAPK leads to release of the MAP2K catalytic machinery, explaining the mechanism of many disease-causing mutations, and ERK2 release is not required for nucleotide exchange, suggesting a processive mechanism. Our data advance the understanding of MAPK signalling and provide a starting point for drug development.
External linksbioRxiv / PubMed:41648251 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.17 - 3.6 Å
Structure data

56418

9tyg

EMDB-56418, PDB-9tyg:
Structure of the MAP2K MEK1 in an inactive conformation in complex with its substrate MAPK ERK2
Method: EM (single particle) / Resolution: 2.9 Å

56419

9tyh

EMDB-56419, PDB-9tyh:
Structure of the MAP2K MEK1 in an active conformation in complex with its substrate MAPK ERK2
Method: EM (single particle) / Resolution: 3.4 Å

56420

9tyi

EMDB-56420, PDB-9tyi:
Structure of the MAP2K MEK1 without bound nucleotide in complex with its substrate MAPK ERK2
Method: EM (single particle) / Resolution: 3.6 Å

PDB-9tu0:
Crystal structure of human ERK1 in complex with the KIM1 motif of the T. gondii protein GRA24
Method: X-RAY DIFFRACTION / Resolution: 2.17 Å

Chemicals

ChemComp-SO4:
SULFATE ION

ChemComp-HOH:
WATER

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

Source
  • homo sapiens (human)
  • toxoplasma gondii me49 (eukaryote)
  • toxoplasma gondii (eukaryote)
KeywordsTRANSFERASE / phosphoryl transfer / kinase / MAPK / GRA24 / toxoplasma / SIGNALING PROTEIN / protein kinases / MAP2K / cancer signaling

+
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