[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

TitleA small signaling domain controls PPIP5K phosphatase activity in phosphate homeostasis.
Journal, issue, pagesNat Commun, Vol. 16, Page 1753-1753, Year 2025
Publish dateSep 11, 2024 (structure data deposition date)
AuthorsRaia, P. / Lee, K. / Bartsch, S.M. / Rico-Resendiz, F. / Portugal-Calisto, D. / Vadas, O. / Panse, V.G. / Fiedler, D. / Hothorn, M.
External linksNat Commun / PubMed:39966396
MethodsX-ray diffraction
Resolution1.18 - 3.4 Å
Structure data

PDB-9gr8:
Crystal structure of the N-terminal kinase domain from Saccharomyces cerevisiae Vip1 in complex with ADP.
Method: X-RAY DIFFRACTION / Resolution: 1.18 Å

PDB-9grh:
Crystal structure of the C-terminal phosphatase domain from Saccharomyces cerevisiae Vip1 (apo)
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-9grn:
Crystal structure of the engineered C-terminal phosphatase domain from Saccharomyces cerevisiae Vip1 (apo, loop deletion residues 848-918)
Method: X-RAY DIFFRACTION / Resolution: 3.4 Å

PDB-9gro:
Crystal structure of the engineered C-terminal phosphatase domain from Saccharomyces cerevisiae Vip1 in complex with 1,5-InsP8 (phosphatase dead mutant, loop deletion residues 848-918)
Method: X-RAY DIFFRACTION / Resolution: 2.36 Å

Chemicals

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

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-HOH:
WATER

ChemComp-ZN:
Unknown entry

ChemComp-GOL:
GLYCEROL

ChemComp-LPC:
[1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE

ChemComp-ACT:
ACETATE ION

ChemComp-SPM:
SPERMINE

ChemComp-ORN:
L-ornithine

ChemComp-PUT:
1,4-DIAMINOBUTANE

ChemComp-I8P:
(1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)]

ChemComp-1JW:
(2S)-hexane-1,2,6-triol

Source
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsBIOSYNTHETIC PROTEIN / Inositol pyrophosphate / inositol pyrophosphate phosphatase / histidine acid phosphatase / phytase / enzyme mechanism / GAF domain / phosphate homeostasis

+
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