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- EMDB-24413: Structure of the S. cerevisiae P4B ATPase lipid flippase in the E... -

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Basic information

Entry
Database: EMDB / ID: EMD-24413
TitleStructure of the S. cerevisiae P4B ATPase lipid flippase in the E2P state
Map dataCryo-EM 3D map of S. cerevisiae P4B ATPase lipid flippase in the E2P state
Sample
  • Complex: P4B ATPase lipid flippase in the E2P state
    • Protein or peptide: Probable phospholipid-transporting ATPase NEO1
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
KeywordsP4B ATPase lipid flippase / TRANSLOCASE
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 / phosphatidylethanolamine flippase activity / vacuole organization / 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 / phosphatidylethanolamine flippase activity / vacuole organization / P-type phospholipid transporter / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phospholipid translocation / trans-Golgi network / endocytosis / protein transport / late endosome / 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
Phospholipid-transporting ATPase NEO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsBai L / Jain BK
Funding support United States, 1 items
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, 2021-
Header (metadata) releaseSep 29, 2021-
Map releaseSep 29, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0136
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0136
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rd6
  • Surface level: 0.0136
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24413.png

Downloads & links

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Map

FileDownload / File: emd_24413.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM 3D map of S. cerevisiae P4B ATPase lipid flippase in the E2P state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 280 pix.
= 231.28 Å		0.83 Å/pix.
x 280 pix.
= 231.28 Å		0.83 Å/pix.
x 280 pix.
= 231.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0136 / Movie #1: 0.0136
Minimum - Maximum-0.065730646 - 0.09873478
Average (Standard dev.)-0.000011003475 (±0.0024893372)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 231.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8260.8260.826
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z231.280231.280231.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0660.099-0.000

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Supplemental data

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Sample components

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Entire : P4B ATPase lipid flippase in the E2P state

EntireName: P4B ATPase lipid flippase in the E2P state
Components
  • Complex: P4B ATPase lipid flippase in the E2P state
    • Protein or peptide: Probable phospholipid-transporting ATPase NEO1
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: P4B ATPase lipid flippase in the E2P state

SupramoleculeName: P4B ATPase lipid flippase in the E2P state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Probable phospholipid-transporting ATPase NEO1

MacromoleculeName: Probable phospholipid-transporting ATPase NEO1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type phospholipid transporter
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 130.363492 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MPNPPSFKSH KQNLFNSNNN QHANSVDSFD LHLDDSFDAA LDSLQINNNP EPLSKHNTVG DRESFEMRTV DDLDNFSNHS SDSHRKSSN TDTHPLMYDN RLSQDDNFKF TNIASSPPSS SNNIFSKALS YLKVSNTKNW SKFGSPIELS DQHIEREIHP D TTPVYDRN ...String:
MPNPPSFKSH KQNLFNSNNN QHANSVDSFD LHLDDSFDAA LDSLQINNNP EPLSKHNTVG DRESFEMRTV DDLDNFSNHS SDSHRKSSN TDTHPLMYDN RLSQDDNFKF TNIASSPPSS SNNIFSKALS YLKVSNTKNW SKFGSPIELS DQHIEREIHP D TTPVYDRN RYVSNELSNA KYNAVTFVPT LLYEQFKFFY NLYFLVVALS QAVPALRIGY LSSYIVPLAF VLTVTMAKEA ID DIQRRRR DRESNNELYH VITRNRSIPS KDLKVGDLIK VHKGDRIPAD LVLLQSSEPS GESFIKTDQL DGETDWKLRV ACP LTQNLS ENDLINRISI TASAPEKSIH KFLGKVTYKD STSNPLSVDN TLWANTVLAS SGFCIACVVY TGRDTRQAMN TTTA KVKTG LLELEINSIS KILCACVFAL SILLVAFAGF HNDDWYIDIL RYLILFSTII PVSLRVNLDL AKSVYAHQIE HDKTI PETI VRTSTIPEDL GRIEYLLSDK TGTLTQNDMQ LKKIHLGTVS YTSETLDIVS DYVQSLVSSK NDSLNNSKVA LSTTRK DMS FRVRDMILTL AICHNVTPTF EDDELTYQAA SPDEIAIVKF TESVGLSLFK RDRHSISLLH EHSGKTLNYE ILQVFPF NS DSKRMGIIVR DEQLDEYWFM QKGADTVMSK IVESNDWLEE ETGNMAREGL RTLVIGRKKL NKKIYEQFQK EYNDASLS M LNRDQQMSQV ITKYLEHDLE LLGLTGVEDK LQKDVKSSIE LLRNAGIKIW MLTGDKVETA RCVSISAKLI SRGQYVHTI TKVTRPEGAF NQLEYLKINR NACLLIDGES LGMFLKHYEQ EFFDVVVHLP TVIACRCTPQ QKADVALVIR KMTGKRVCCI GDGGNDVSM IQCADVGVGI VGKEGKQASL AADFSITQFC HLTELLLWHG RNSYKRSAKL AQFVMHRGLI IAICQAVYSI C SLFEPIAL YQGWLMVGYA TCYTMAPVFS LTLDHDIEES LTKIYPELYK ELTEGKSLSY KTFFVWVLLS LFQGSVIQLF SQ AFTSLLD TDFTRMVAIS FTALVVNELI MVALEIYTWN KTMLVTEIAT LLFYIVSVPF LGDYFDLGYM TTVNYYAGLL VIL LISIFP VWTAKAIYRR LHPPSYAKVQ EFATP

UniProtKB: Phospholipid-transporting ATPase NEO1

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Macromolecule #2: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1279510
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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