[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 for Membrane Recruitment by the PX and C2 Domains of Class II Phosphoinositide 3-Kinase-C2α.
Journal, issue, pagesStructure, Vol. 26, Issue 12, Page 1612-11625.e4, Year 2018
Publish dateDec 4, 2018
AuthorsKai-En Chen / Vikas A Tillu / Mintu Chandra / Brett M Collins /
PubMed AbstractPhosphorylation of phosphoinositides by the class II phosphatidylinositol 3-kinase (PI3K) PI3K-C2α is essential for many processes, including neuroexocytosis and formation of clathrin-coated ...Phosphorylation of phosphoinositides by the class II phosphatidylinositol 3-kinase (PI3K) PI3K-C2α is essential for many processes, including neuroexocytosis and formation of clathrin-coated vesicles. A defining feature of the class II PI3Ks is a C-terminal module composed of phox-homology (PX) and C2 membrane interacting domains; however, the mechanisms that control their specific cellular localization remain poorly understood. Here we report the crystal structure of the C2 domain of PI3K-C2α in complex with the phosphoinositide head-group mimic inositol hexaphosphate, revealing two distinct pockets for membrane binding. The C2 domain preferentially binds to phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol (3,4,5)-trisphosphate, and low-resolution structures of the combined PX-C2 module by small-angle X-ray scattering reveal a compact conformation in which cooperative lipid binding by each domain binding can occur. Finally, we demonstrate an unexpected role for calcium in perturbing the membrane interactions of the PX-C2 module, which we speculate may be important for regulating the activity of PI3K-C2α.
External linksStructure / PubMed:30293811
MethodsSAS (X-ray synchrotron) / X-ray diffraction
Resolution1.678 - 2.604 Å
Structure data

SASDD66:
Phox homologue (PX) - C2 domains of human phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha (PI3KC2α)
Method: SAXS/SANS

SASDD76:
Phox Homologue (PX) - C2 domains of human phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha (PI3KC2α) in complex with inositol-hexaphosphate (IP6)
Method: SAXS/SANS

PDB-6bty:
Crystal structure of the PI3KC2alpha C2 domain in space group P41212
Method: X-RAY DIFFRACTION / Resolution: 1.678 Å

PDB-6btz:
Crystal structure of the PI3KC2alpha C2 domain in space group C121
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-6bu0:
Crystal structure of the PI3KC2alpha C2 domain in complex with IP6
Method: X-RAY DIFFRACTION / Resolution: 2.427 Å

PDB-6bub:
Crystal structure of the PI3KC2alpha PX domain in space group P432
Method: X-RAY DIFFRACTION / Resolution: 2.604 Å

Chemicals

ChemComp-O4B:
1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / 18-Crown-6

ChemComp-HOH:
WATER / Water

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-FMT:
FORMIC ACID / Formic acid

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE / Phytic acid

Source
  • homo sapiens (human)
KeywordsTRANSFERASE / C2 domain / lipid binding / phosphoinositide / PI3-kinase / PX domain

+
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