7RD8 | pdb_00007rd8

Structure of the S. cerevisiae P4B ATPase lipid flippase in the E1-ATP state

• PDB DOI: https://doi.org/10.2210/pdb7RD8/pdb
• EM Map EMD-24415: EMDB EMDataResource

• Classification: TRANSLOCASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2021-07-09 Released: 2021-09-29 
• Deposition Author(s): Bai, L., Jain, B.K., You, Q., Duan, H.D., Graham, T.R., Li, H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.64 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of the P4B ATPase lipid flippase activity.

Bai, L., Jain, B.K., You, Q., Duan, H.D., Takar, M., Graham, T.R., Li, H.

(2021) Nat Commun 12: 5963-5963

• PubMed: 34645814 
• DOI: https://doi.org/10.1038/s41467-021-26273-0
• Primary Citation Related Structures: 
  7RD6, 7RD7, 7RD8


• PubMed Abstract: 
  

  P4 ATPases are lipid flippases that are phylogenetically grouped into P4A, P4B and P4C clades. The P4A ATPases are heterodimers composed of a catalytic α-subunit and accessory β-subunit, and the structures of several heterodimeric flippases have been reported. The S. cerevisiae Neo1 and its orthologs represent the P4B ATPases, which function as monomeric flippases without a β-subunit. It has been unclear whether monomeric flippases retain the architecture and transport mechanism of the dimeric flippases. Here we report the structure of a P4B ATPase, Neo1, in its E1-ATP, E2P-transition, and E2P states. The structure reveals a conserved architecture as well as highly similar functional intermediate states relative to dimeric flippases. Consistently, structure-guided mutagenesis of residues in the proposed substrate translocation path disrupted Neo1's ability to establish membrane asymmetry. These observations indicate that evolutionarily distant P4 ATPases use a structurally conserved mechanism for substrate transport.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China. [e-mail].
Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. [e-mail].
Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 130.89 kDa 
• Atom Count: 7,417 
• Modeled Residue Count: 929 
• Deposited Residue Count: 1,151 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable phospholipid-transporting ATPase NEO1	A	1,151	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: NEO1, YIL048W EC: 7.6.2.1 Membrane Entity: Yes
UniProt
Find proteins for P40527 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40527  Go to UniProtKB:  P40527

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACP	B [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.64 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-29 
Deposition Author(s): Bai, L., Jain, B.K., You, Q., Duan, H.D., Graham, T.R., Li, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	CA231466 to H.L. and GM107978 to T.R.G.

Revision History  

• Version 1.0: 2021-09-29
  Type: Initial release
  
• Version 1.1: 2021-10-27
  Changes: Database references
• Version 1.2: 2024-06-05
  Changes: Data collection
• Version 1.3: 2025-05-28
  Changes: Data collection, Structure summary