6ROJ

Cryo-EM structure of the activated Drs2p-Cdc50p

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Structure and autoregulation of a P4-ATPase lipid flippase.

Timcenko, M., Lyons, J.A., Januliene, D., Ulstrup, J.J., Dieudonne, T., Montigny, C., Ash, M.R., Karlsen, J.L., Boesen, T., Kuhlbrandt, W., Lenoir, G., Moeller, A., Nissen, P.

(2019) Nature 571: 366-370

  • DOI: 10.1038/s41586-019-1344-7
  • Primary Citation of Related Structures:  
    6ROH, 6ROI, 6ROJ

  • PubMed Abstract: 

    • Type 4 P-type ATPases (P4-ATPases) are lipid flippases that drive the active transport of phospholipids from exoplasmic or luminal leaflets to cytosolic leaflets of eukaryotic membranes. The molecular architecture of P4-ATPases and the mechanism through which they recognize and transport lipids have remained unknown ...

    Type 4 P-type ATPases (P4-ATPases) are lipid flippases that drive the active transport of phospholipids from exoplasmic or luminal leaflets to cytosolic leaflets of eukaryotic membranes. The molecular architecture of P4-ATPases and the mechanism through which they recognize and transport lipids have remained unknown. Here we describe the cryo-electron microscopy structure of the P4-ATPase Drs2p-Cdc50p, a Saccharomyces cerevisiae lipid flippase that is specific to phosphatidylserine and phosphatidylethanolamine. Drs2p-Cdc50p is autoinhibited by the C-terminal tail of Drs2p, and activated by the lipid phosphatidylinositol-4-phosphate (PtdIns4P or PI4P). We present three structures that represent the complex in an autoinhibited, an intermediate and a fully activated state. The analysis highlights specific features of P4-ATPases and reveals sites of autoinhibition and PI4P-dependent activation. We also observe a putative lipid translocation pathway in this flippase that involves a conserved PISL motif in transmembrane segment 4 and polar residues of transmembrane segments 2 and 5, in particular Lys1018, in the centre of the lipid bilayer.

    Organizational Affiliation: 

    DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark. pn@mbg.au.dk.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable phospholipid-transporting ATPase DRS2,Oxaloacetate decarboxylase alpha chainA1465Saccharomyces cerevisiae S288C, Klebsiella pneumoniae
This entity is chimeric		Mutation(s): 0 
Gene Names: DRS2, YAL026C, FUN38, oadA
EC: 7.6.2.1 (PDB Primary Data), 7.2.4.2 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for P13187 (Klebsiella pneumoniae)
Explore P13187 
Go to UniProtKB:  P13187
Find proteins for P39524 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39524 
Go to UniProtKB:  P39524
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP13187P39524
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division control protein 50B [auth C]413Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC50, YCR094W, YCR94W
Membrane Entity: Yes 
UniProt
Find proteins for P25656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25656 
Go to UniProtKB:  P25656
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25656
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth B],
E		4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G31886NL
GlyCosmos:  G31886NL
GlyGen:  G31886NL
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2Y5 (Subject of Investigation/LOI)
Query on 2Y5
Download Ideal Coordinates CCD File 
G [auth A](2R)-1-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate
C47 H84 O16 P2
ROKMWIUSHIHOGI-BWTMTLBLSA-N		 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG
Download Ideal Coordinates CCD File 
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BFD
Query on BFD		A L-PEPTIDE LINKINGC4 H6 Be F3 N O4ASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Danish Council for Independent ResearchDenmark0602-02912B
LundbeckfondenDenmarkR171-2014-663
LundbeckfondenDenmarkR209-2015-2704
LundbeckfondenDenmark2015-2666
French National Research AgencyFranceANR-14-CE09-0022
French Infrastructure for Integrated Structural BiologyFranceANR-10-INSB-05

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary