7BSQ

Cryo-EM structure of a human ATP11C-CDC50A flippase in E1AlF-ADP state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Transport Cycle of Plasma Membrane Flippase ATP11C by Cryo-EM.

Nakanishi, H.Nishizawa, T.Segawa, K.Nureki, O.Fujiyoshi, Y.Nagata, S.Abe, K.

(2020) Cell Rep 32: 108208-108208

  • DOI: 10.1016/j.celrep.2020.108208
  • Primary Citation of Related Structures:  
    7BSS, 7BSP, 7BSQ, 7BSV, 7BSW, 7BSU

  • PubMed Abstract: 
  • ATP11C, a plasma membrane phospholipid flippase, maintains the asymmetric distribution of phosphatidylserine accumulated in the inner leaflet. Caspase-dependent inactivation of ATP11C is essential for an apoptotic "eat me" signal, phosphatidylserine exposure, which prompts phagocytes to engulf cells ...

    ATP11C, a plasma membrane phospholipid flippase, maintains the asymmetric distribution of phosphatidylserine accumulated in the inner leaflet. Caspase-dependent inactivation of ATP11C is essential for an apoptotic "eat me" signal, phosphatidylserine exposure, which prompts phagocytes to engulf cells. We show six cryo-EM structures of ATP11C at 3.0-4.0 Å resolution in five different states of the transport cycle. A structural comparison reveals phosphorylation-driven domain movements coupled with phospholipid binding. Three structures of phospholipid-bound states visualize phospholipid translocation accompanied by the rearrangement of transmembrane helices and an unwound portion at the occlusion site, and thus they detail the basis for head group recognition and the locality of the protein-bound acyl chains in transmembrane grooves. Invariant Lys880 and the surrounding hydrogen-bond network serve as a pivot point for helix bending and precise P domain inclination, which is crucial for dephosphorylation. The structures detail key features of phospholipid translocation by ATP11C, and a common basic mechanism for flippases is emerging.


    Organizational Affiliation

    Cellular and Structural Physiology Institute, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan. Electronic address: kabe@cespi.nagoya-u.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP11CA1084Homo sapiensMutation(s): 0 
Gene Names: ATP11CATPIGATPIQ
EC: 7.6.2.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NB49 (Homo sapiens)
Explore Q8NB49 
Go to UniProtKB:  Q8NB49
PHAROS:  Q8NB49
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CDC50AB [auth C]361Homo sapiensMutation(s): 0 
Gene Names: TMEM30AC6orf67CDC50A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NV96 (Homo sapiens)
Explore Q9NV96 
Go to UniProtKB:  Q9NV96
PHAROS:  Q9NV96
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth B]3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
E [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth C], I [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ALF
Query on ALF

Download Ideal Coordinates CCD File 
D [auth A]TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJCR14M4
Japan Agency for Medical Research and Development (AMED)Japan--
Japan Society for the Promotion of Science (JSPS)Japan17H03653

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references