[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

TitleThe structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 2915, Year 2022
Publish dateMay 25, 2022
AuthorsAlmutasem Saleh / Yasunori Noguchi / Ricardo Aramayo / Marina E Ivanova / Kathryn M Stevens / Alex Montoya / S Sunidhi / Nicolas Lopez Carranza / Marcin J Skwark / Christian Speck /
PubMed AbstractThe controlled assembly of replication forks is critical for genome stability. The Dbf4-dependent Cdc7 kinase (DDK) initiates replisome assembly by phosphorylating the MCM2-7 replicative helicase at ...The controlled assembly of replication forks is critical for genome stability. The Dbf4-dependent Cdc7 kinase (DDK) initiates replisome assembly by phosphorylating the MCM2-7 replicative helicase at the N-terminal tails of Mcm2, Mcm4 and Mcm6. At present, it remains poorly understood how DDK docks onto the helicase and how the kinase targets distal Mcm subunits for phosphorylation. Using cryo-electron microscopy and biochemical analysis we discovered that an interaction between the HBRCT domain of Dbf4 with Mcm2 serves as an anchoring point, which supports binding of DDK across the MCM2-7 double-hexamer interface and phosphorylation of Mcm4 on the opposite hexamer. Moreover, a rotation of DDK along its anchoring point allows phosphorylation of Mcm2 and Mcm6. In summary, our work provides fundamental insights into DDK structure, control and selective activation of the MCM2-7 helicase during DNA replication. Importantly, these insights can be exploited for development of novel DDK inhibitors.
External linksNat Commun / PubMed:35614055 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 18.0 Å
Structure data

13619

7pt6

EMDB-13619: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state III (composite map)
PDB-7pt6: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state III
Method: EM (single particle) / Resolution: 3.2 Å

13620

7pt7

EMDB-13620, PDB-7pt7:
Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, state I
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-13621: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state III (B1 map)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-13622: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state III (B2 map)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-13623: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state III (B3 map)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-13624: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state III (3D auto-refined map)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-13629: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state II (composite map)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-13631: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state II (B1 map)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-13635: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state II (B2 map)
Method: EM (single particle) / Resolution: 5.2 Å

EMDB-13640: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state II (3D auto-refined map)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-13644: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state I (3D auto-refined map)
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-13645: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, state I (B1 map)
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-13646: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, state I (B2 map)
Method: EM (single particle) / Resolution: 4.4 Å

EMDB-13647: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, state I (3D auto-refined map)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-13648: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, swiveled state (3D auto-refined map)
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-13649: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, swiveled state A (binned 3D auto-refined map)
Method: EM (single particle) / Resolution: 9.0 Å

EMDB-13650: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, swiveled state B (binned 3D auto-refined map)
Method: EM (single particle) / Resolution: 18.0 Å

EMDB-13651: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, swiveled state C (binned 3D auto-refined map)
Method: EM (single particle) / Resolution: 9.0 Å

EMDB-13652: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, swiveled state D (binned 3D auto-refined map)
Method: EM (single particle) / Resolution: 9.0 Å

EMDB-13653: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, swiveled state E (binned 3D auto-refined map)
Method: EM (single particle) / Resolution: 12.0 Å

EMDB-13655: Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, swiveled state F (binned 3D auto-refined map)
Method: EM (single particle) / Resolution: 13.0 Å

EMDB-13656: Structure of double-stranded DNA-bound MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATP (3D auto-refined map)
Method: EM (single particle) / Resolution: 9.1 Å

EMDB-13657: Structure of double-stranded DNA-bound MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATP (B1 map)
Method: EM (single particle) / Resolution: 8.3 Å

EMDB-13658: Structure of double-stranded DNA-bound MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATP (B2 map)
Method: EM (single particle) / Resolution: 11.0 Å

EMDB-13659: Structure of double-stranded DNA-bound MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATP (B3 map)
Method: EM (single particle) / Resolution: 9.8 Å

Chemicals

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

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

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

Source
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • Saccharomyces cerevisiae (brewer's yeast)
  • synthetic construct (others)
KeywordsREPLICATION / Helicase / Activation / Kinase / Phosphorylation

+
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