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- EMDB-30169: Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdEtn-occ... -

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Basic information

Entry
Database: EMDB / ID: EMD-30169
TitleCryo-EM structure of a human ATP11C-CDC50A flippase in PtdEtn-occluded E2-AlF state
Map data
Sample
  • Complex: human ATP11C-CDC50A flippase
    • Protein or peptide: ATP11C
    • Protein or peptide: CDC50A
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose
Function / homology
Function and homology information


positive regulation of phospholipid translocation / aminophospholipid transport / aminophospholipid flippase activity / phosphatidylserine flippase activity / protein localization to endosome / ATPase-coupled intramembrane lipid transporter activity / phospholipid-translocating ATPase complex / phosphatidylserine floppase activity / positive regulation of protein exit from endoplasmic reticulum / phosphatidylethanolamine flippase activity ...positive regulation of phospholipid translocation / aminophospholipid transport / aminophospholipid flippase activity / phosphatidylserine flippase activity / protein localization to endosome / ATPase-coupled intramembrane lipid transporter activity / phospholipid-translocating ATPase complex / phosphatidylserine floppase activity / positive regulation of protein exit from endoplasmic reticulum / phosphatidylethanolamine flippase activity / xenobiotic transmembrane transport / P-type phospholipid transporter / phospholipid translocation / azurophil granule membrane / transport vesicle membrane / Ion transport by P-type ATPases / specific granule membrane / recycling endosome / positive regulation of neuron projection development / recycling endosome membrane / late endosome membrane / early endosome membrane / monoatomic ion transmembrane transport / apical plasma membrane / lysosomal membrane / Neutrophil degranulation / endoplasmic reticulum membrane / structural molecule activity / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
CDC50/LEM3 family / LEM3 (ligand-effect modulator 3) family / CDC50 family / 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 ...CDC50/LEM3 family / LEM3 (ligand-effect modulator 3) family / CDC50 family / 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 IG / Cell cycle control protein 50A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsAbe K / Nishizawa T / Nakanishi H
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR14M4 Japan
Japan Society for the Promotion of Science (JSPS)17H03653 Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Cell Rep / Year: 2020
Title: Transport Cycle of Plasma Membrane Flippase ATP11C by Cryo-EM.
Authors: Hanayo Nakanishi / Tomohiro Nishizawa / Katsumori Segawa / Osamu Nureki / Yoshinori Fujiyoshi / Shigekazu Nagata / Kazuhiro Abe /
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 ...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.
History
DepositionMar 31, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bsw
  • Surface level: 0.036315891
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30169.png

Downloads & links

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Map

FileDownload / File: emd_30169.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 160 pix.
= 216. Å		1.35 Å/pix.
x 160 pix.
= 216. Å		1.35 Å/pix.
x 160 pix.
= 216. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0158 / Movie #1: 0.04
Minimum - Maximum-0.16585647 - 0.26740387
Average (Standard dev.)0.0008292035 (±0.007874824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 216.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z216.000216.000216.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ510510510
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.1660.2670.001

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Supplemental data

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Sample components

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Entire : human ATP11C-CDC50A flippase

EntireName: human ATP11C-CDC50A flippase
Components
  • Complex: human ATP11C-CDC50A flippase
    • Protein or peptide: ATP11C
    • Protein or peptide: CDC50A
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: human ATP11C-CDC50A flippase

SupramoleculeName: human ATP11C-CDC50A flippase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Expi293
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: ATP11C

MacromoleculeName: ATP11C / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 124.403617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RFCAGEEKRV GTRTVFVGNH PVSETEAYIA QRFCDNRIVS SKYTLWNFLP KNLFEQFRRI ANFYFLIIFL VQVTVDTPTS PVTSGLPLF FVITVTAIKQ GYEDWLRHRA DNEVNKSTVY IIENAKRVRK ESEKIKVGDV VEVQADETFP CDLILLSSCT T DGTCYVTT ...String:
RFCAGEEKRV GTRTVFVGNH PVSETEAYIA QRFCDNRIVS SKYTLWNFLP KNLFEQFRRI ANFYFLIIFL VQVTVDTPTS PVTSGLPLF FVITVTAIKQ GYEDWLRHRA DNEVNKSTVY IIENAKRVRK ESEKIKVGDV VEVQADETFP CDLILLSSCT T DGTCYVTT ASLDGESNCK THYAVRDTIA LCTAESIDTL RAAIECEQPQ PDLYKFVGRI NIYSNSLEAV ARSLGPENLL LK GATLKNT EKIYGVAVYT GMETKMALNY QGKSQKRSAV EKSINAFLIV YLFILLTKAA VCTTLKYVWQ STPYNDEPWY NQK TQKERE TLKVLKMFTD FLSFMVLFNF IIPVSMYVTV EMQKFLGSFF ISWDKDFYDE EINEGALVNT SDLNEELGQV DYVF TDKTG TLTENSMEFI ECCIDGHKYK GVTQEVDGLS QTDGTLTYFD KVDKNREELF LRALCLCHTV EIKTNDAVDG ATESA ELTY ISSSPDEIAL VKGAKRYGFT FLGNRNGYMR VENQRKEIEE YELLHTLNFD AVRRRMSVIV KTQEGDILLF CKGADS AVF PRVQNHEIEL TKVHVERNAM DGYRTLCVAF KEIAPDDYER INRQLIEAKM ALQDREEKME KVFDDIETNM NLIGATA VE DKLQDQAAET IEALHAAGLK VWVLTGDKME TAKSTCYACR LFQTNTELLE LTTKTIEESE RKEDRLHELL IEYRKKLL H EFPKSTRSFK KAWTEHQEYG LIIDGSTLSL ILNSSQDSSS NNYKSIFLQI CMKCTAVLCC RMAPLQKAQI VRMVKNLKG SPITLSIGDG ANDVSMILES HVGIGIKGKE GRQAARNSDY SVPKFKHLKK LLLAHGHLYY VRIAHLVQYF FYKNLCFILP QFLYQFFCG FSQQPLYDAA YLTMYNICFT SLPILAYSLL EQHINIDTLT SDPRLYMKIS GNAMLQLGPF LYWTFLAAFE G TVFFFGTY FLFQTASLEE NGKVYGNWTF GTIVFTVLVF TVTLKLALDT RFWTWINHFV IWGSLAFYVF FSFFWGGIIW PF LKQQRMY FVFAQMLSSV STWLAIILLI FISLFPEILL IVLKNVR

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Macromolecule #2: CDC50A

MacromoleculeName: CDC50A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.900801 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAMNYNAKDE VDGGPPCAPG GTAKTRRPDN TAFKQQRLPA WQPILTAGTV LPIFFIIGLI FIPIGIGIFV TSNNIREIEI DYTGTEPSS PCNKCLSPDV TPCFCTINFT LEKSFEGNVF MYYGLSNFYQ NHRRYVKSRD DSQLNGDSSA LLNPSKECEP Y RRNEDKPI ...String:
MAMNYNAKDE VDGGPPCAPG GTAKTRRPDN TAFKQQRLPA WQPILTAGTV LPIFFIIGLI FIPIGIGIFV TSNNIREIEI DYTGTEPSS PCNKCLSPDV TPCFCTINFT LEKSFEGNVF MYYGLSNFYQ NHRRYVKSRD DSQLNGDSSA LLNPSKECEP Y RRNEDKPI APCGAIMNSM FNDTLELFLI GQDSYPIPIA LKKKGIAWWT DKNVKFRNPP GGDNLEERFK GTTKPVNWLK PV YMLDSDP DNNGFINEDF IVWMRTAALP TFRKLYRLIE RKSDLHPTLP AGRYWLNVTY NYPVHYFDGR KRMILSTISW MGG KNPFLG IAYIAVGSIS FLLGVVLLVI NHKYRNSSNT ADITI

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Macromolecule #3: TETRAFLUOROALUMINATE ION

MacromoleculeName: TETRAFLUOROALUMINATE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ALF
Molecular weightTheoretical: 102.975 Da
Chemical component information

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

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Macromolecule #4: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 4 / Number of copies: 1 / Formula: PEE
Molecular weightTheoretical: 749.073 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #6: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 6 / Number of copies: 1 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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

Concentration8 mg/mL
BufferpH: 6.5
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 400000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7bsw:
Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdEtn-occluded E2-AlF state

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