[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

TitleCryo-EM structure of the ATP11C Q79E mutant reveals the structural basis for altered Phospholipid recognition.
Journal, issue, pagesJ Biol Chem, Vol. 302, Issue 1, Page 110935, Year 2025
Publish dateNov 12, 2025
AuthorsYuheng Qian / Chai C Gopalasingam / Christoph Gerle / Hideki Shigematsu / Kazuhiro Abe / Atsunori Oshima /
PubMed AbstractClosely related P4-ATPases, ATP11A and ATP11C, act as major phospholipid flippases in the plasma membrane of mammalian cells, with strict substrate specificity for phosphatidylserine (PS) and ...Closely related P4-ATPases, ATP11A and ATP11C, act as major phospholipid flippases in the plasma membrane of mammalian cells, with strict substrate specificity for phosphatidylserine (PS) and phosphatidylethanolamine (PE), but not for phosphatidylcholine (PC), thereby contributing to the asymmetric distribution of PS and PE across bilayers. A previously reported disease-associated Q84E mutation in ATP11A confers the ability to flip PC, implicating the involvement of this conserved residue in substrate specificity. We performed cryo-EM analysis for the equivalent mutant Q79E of ATP11C to address the structural basis for its unusual substrate specificity. Measurement of ATPase activity revealed that the ATP11C Q79E mutant retained PS-dependent activity, whilst gaining robust PC-dependent activity, indicative of expanded substrate specificity, consistent with reported properties in ATP11A Q84E. The cryo-EM structure of ATP11C Q79E mutant in the PC-occluded E2-P state revealed a PC molecule in a reshaped binding pocket. Due to the Q79E mutation and associated conformational changes in its surrounding residues, including Ser91and Asn352, the binding pocket has additional space to accommodate the bulky choline headgroup. Our results provide structural and functional insights into how a single point mutation can alter substrate specificity in a P4-ATPase.
External linksJ Biol Chem / PubMed:41237907 / PubMed Central
MethodsEM (single particle)
Resolution2.39 - 3.4 Å
Structure data

65136

9vkg

EMDB-65136, PDB-9vkg:
Cryo-EM structure of a human flippase mutant ATP11C Q79E-CDC50A in PtdCho-occluded E2-AlF state
Method: EM (single particle) / Resolution: 2.39 Å

65217

9vnt

EMDB-65217, PDB-9vnt:
Cryo-EM structure of a human flippase mutant ATP11C Q79E-CDC50A in PtdSer-occluded E2P-AlF state
Method: EM (single particle) / Resolution: 2.51 Å

65258

9vq2

EMDB-65258, PDB-9vq2:
Cryo-EM structure of a human flippase mutant ATP11C Q79A-CDC50A in the PtdSer-occluded E2-AlF state
Method: EM (single particle) / Resolution: 3.4 Å

65302

9vsl

EMDB-65302, PDB-9vsl:
Cryo-EM structrure of a human flippase mutant ATP11C Q79E-CDC50A in PtdCho-open E2-BeF state
Method: EM (single particle) / Resolution: 2.88 Å

Chemicals

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

ChemComp-MG:
Unknown entry

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-HOH:
WATER

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

Source
  • homo sapiens (human)
KeywordsTRANSPORT PROTEIN / Lipid transporter flippase / PC bound E2P state / PS bound E2P state / PC bound E2P BeF state

+
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