[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 structures capture the transport cycle of the P4-ATPase flippase.
Journal, issue, pagesScience, Vol. 365, Issue 6458, Page 1149-1155, Year 2019
Publish dateSep 13, 2019
AuthorsMasahiro Hiraizumi / Keitaro Yamashita / Tomohiro Nishizawa / Osamu Nureki /
PubMed AbstractIn eukaryotic membranes, type IV P-type adenosine triphosphatases (P4-ATPases) mediate the translocation of phospholipids from the outer to the inner leaflet and maintain lipid asymmetry, which is ...In eukaryotic membranes, type IV P-type adenosine triphosphatases (P4-ATPases) mediate the translocation of phospholipids from the outer to the inner leaflet and maintain lipid asymmetry, which is critical for membrane trafficking and signaling pathways. Here, we report the cryo-electron microscopy structures of six distinct intermediates of the human ATP8A1-CDC50a heterocomplex at resolutions of 2.6 to 3.3 angstroms, elucidating the lipid translocation cycle of this P4-ATPase. ATP-dependent phosphorylation induces a large rotational movement of the actuator domain around the phosphorylation site in the phosphorylation domain, accompanied by lateral shifts of the first and second transmembrane helices, thereby allowing phosphatidylserine binding. The phospholipid head group passes through the hydrophilic cleft, while the acyl chain is exposed toward the lipid environment. These findings advance our understanding of the flippase mechanism and the disease-associated mutants of P4-ATPases.
External linksScience / PubMed:31416931
MethodsEM (single particle)
Resolution2.63 - 3.42 Å
Structure data

EMDB-9931, PDB-6k7g:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1 state class1)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-9932, PDB-6k7h:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1 state class2)
Method: EM (single particle) / Resolution: 3.22 Å

EMDB-9933:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1 state class3)
Method: EM (single particle) / Resolution: 3.42 Å

EMDB-9934, PDB-6k7i:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1-ATP state class2)
Method: EM (single particle) / Resolution: 3.22 Å

EMDB-9935, PDB-6k7j:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1-ATP state class1)
Method: EM (single particle) / Resolution: 3.08 Å

EMDB-9936:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1-ATP state class3)
Method: EM (single particle) / Resolution: 3.32 Å

EMDB-9937, PDB-6k7k:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1-ADP-Pi state)
Method: EM (single particle) / Resolution: 3.04 Å

EMDB-9938:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2P state class1)
Method: EM (single particle) / Resolution: 2.76 Å

EMDB-9939, PDB-6k7l:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2P state class2)
Method: EM (single particle) / Resolution: 2.83 Å

EMDB-9940:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2P state class3)
Method: EM (single particle) / Resolution: 2.63 Å

EMDB-9941, PDB-6k7m:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2Pi-PL state)
Method: EM (single particle) / Resolution: 2.95 Å

EMDB-9942, PDB-6k7n:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1P state)
Method: EM (single particle) / Resolution: 2.84 Å

Chemicals

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

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

ChemComp-ACP:
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / AMP-PCP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

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

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-D39:
(2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid

Source
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / flippase

+
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