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- PDB-7rd8: Structure of the S. cerevisiae P4B ATPase lipid flippase in the E... -

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Entry
Database: PDB / ID: 7rd8
TitleStructure of the S. cerevisiae P4B ATPase lipid flippase in the E1-ATP state
ComponentsProbable phospholipid-transporting ATPase NEO1
KeywordsTRANSLOCASE / P4B ATPase lipid flippase
Function / homology
Function and homology information


lysophosphatidylserine flippase activity / trans-Golgi network membrane organization / Ion transport by P-type ATPases / phosphatidylserine flippase activity / ATPase-coupled intramembrane lipid transporter activity / phosphatidylserine floppase activity / vacuole organization / phosphatidylethanolamine flippase activity / P-type phospholipid transporter / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ...lysophosphatidylserine flippase activity / trans-Golgi network membrane organization / Ion transport by P-type ATPases / phosphatidylserine flippase activity / ATPase-coupled intramembrane lipid transporter activity / phosphatidylserine floppase activity / vacuole organization / phosphatidylethanolamine flippase activity / P-type phospholipid transporter / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phospholipid translocation / trans-Golgi network / endocytosis / late endosome / protein transport / endosome membrane / endosome / Golgi membrane / Golgi apparatus / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IV / P-type ATPase, C-terminal / P-type ATPase, N-terminal / Phospholipid-translocating ATPase N-terminal / Phospholipid-translocating P-type ATPase C-terminal / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N ...P-type ATPase, subfamily IV / P-type ATPase, C-terminal / P-type ATPase, N-terminal / Phospholipid-translocating ATPase N-terminal / Phospholipid-translocating P-type ATPase C-terminal / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Phospholipid-transporting ATPase NEO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.64 Å
AuthorsBai, L. / Jain, B.K. / You, Q. / Duan, H.D. / Graham, T.R. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)CA231466 to H.L. and GM107978 to T.R.G. United States
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of the P4B ATPase lipid flippase activity.
Authors: Lin Bai / Bhawik K Jain / Qinglong You / H Diessel Duan / Mehmet Takar / Todd R Graham / Huilin Li /
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 ...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.
History
DepositionJul 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Probable phospholipid-transporting ATPase NEO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8933
Polymers130,3631
Non-polymers5302
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area720 Å2
ΔGint-0 kcal/mol
Surface area47390 Å2

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Components

#1: Protein Probable phospholipid-transporting ATPase NEO1


Mass: 130363.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NEO1, YIL048W / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P40527, P-type phospholipid transporter
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: P4B ATPase lipid flippase in the E1-ATP state / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 5.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 264891 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047570
ELECTRON MICROSCOPYf_angle_d0.84110271
ELECTRON MICROSCOPYf_dihedral_angle_d31.2041008
ELECTRON MICROSCOPYf_chiral_restr0.0511215
ELECTRON MICROSCOPYf_plane_restr0.0041268

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