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- PDB-6k7n: Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1P... -

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Entry
Database: PDB / ID: 6k7n
TitleCryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1P state)
Components
  • Cell cycle control protein 50A
  • Phospholipid-transporting ATPase
KeywordsMEMBRANE PROTEIN / flippase
Function / homology
Function and homology information


aminophospholipid translocation / positive regulation of phospholipid translocation / aminophospholipid flippase activity / aminophospholipid transport / chromaffin granule membrane / phosphatidylserine flippase activity / protein localization to endosome / phospholipid-translocating ATPase complex / positive regulation of protein exit from endoplasmic reticulum / phosphatidylserine floppase activity ...aminophospholipid translocation / positive regulation of phospholipid translocation / aminophospholipid flippase activity / aminophospholipid transport / chromaffin granule membrane / phosphatidylserine flippase activity / protein localization to endosome / phospholipid-translocating ATPase complex / positive regulation of protein exit from endoplasmic reticulum / phosphatidylserine floppase activity / ATPase-coupled intramembrane lipid transporter activity / phospholipid transport / xenobiotic transmembrane transport / ATPase-coupled monoatomic cation transmembrane transporter activity / P-type phospholipid transporter / azurophil granule membrane / phospholipid translocation / transport vesicle membrane / organelle membrane / Ion transport by P-type ATPases / synaptic vesicle endocytosis / transport across blood-brain barrier / specific granule membrane / endomembrane system / learning / trans-Golgi network / positive regulation of neuron projection development / synaptic vesicle membrane / late endosome membrane / cytoplasmic vesicle / early endosome membrane / monoatomic ion transmembrane transport / positive regulation of cell migration / apical plasma membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / glutamatergic synapse / structural molecule activity / magnesium ion binding / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol
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 / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / 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 / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / 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
TETRAFLUOROALUMINATE ION / CHOLESTEROL HEMISUCCINATE / Phospholipid-transporting ATPase / Cell cycle control protein 50A / Phospholipid-transporting ATPase IA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsHiraizumi, M. / Yamashita, K. / Nishizawa, T. / Nureki, O.
CitationJournal: Science / Year: 2019
Title: Cryo-EM structures capture the transport cycle of the P4-ATPase flippase.
Authors: Masahiro Hiraizumi / Keitaro Yamashita / Tomohiro Nishizawa / Osamu Nureki /
Abstract: In eukaryotic membranes, type IV P-type adenosine triphosphatases (P4-ATPases) mediate the translocation of phospholipids from the outer to the inner leaflet and maintain lipid asymmetry, which is ...In eukaryotic membranes, type IV P-type adenosine triphosphatases (P4-ATPases) mediate the translocation of phospholipids from the outer to the inner leaflet and maintain lipid asymmetry, which is critical for membrane trafficking and signaling pathways. Here, we report the cryo-electron microscopy structures of six distinct intermediates of the human ATP8A1-CDC50a heterocomplex at resolutions of 2.6 to 3.3 angstroms, elucidating the lipid translocation cycle of this P4-ATPase. ATP-dependent phosphorylation induces a large rotational movement of the actuator domain around the phosphorylation site in the phosphorylation domain, accompanied by lateral shifts of the first and second transmembrane helices, thereby allowing phosphatidylserine binding. The phospholipid head group passes through the hydrophilic cleft, while the acyl chain is exposed toward the lipid environment. These findings advance our understanding of the flippase mechanism and the disease-associated mutants of P4-ATPases.
History
DepositionJun 7, 2019Deposition site: PDBJ / Processing site: PDBJ
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Assembly

Deposited unit
A: Phospholipid-transporting ATPase
C: Cell cycle control protein 50A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,9088
Polymers171,2652
Non-polymers1,6436
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10120 Å2
ΔGint-43 kcal/mol
Surface area56330 Å2

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein Phospholipid-transporting ATPase


Mass: 130537.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
References: UniProt: Q59EX4, UniProt: Q9Y2Q0*PLUS, P-type phospholipid transporter
#2: Protein Cell cycle control protein 50A


Mass: 40727.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC50A / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q9NV96

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Sugars , 2 types, 3 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 3 molecules

#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: ATP8A1-CDC50a / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293F
Buffer solutionpH: 7.5
SpecimenConc.: 4 mg/ml / Embedding 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: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.14_3260refinement
PHENIX1.14_3260refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 242920 / Symmetry type: POINT
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.012610800
ELECTRON MICROSCOPYf_angle_d1.25614674
ELECTRON MICROSCOPYf_chiral_restr0.07171678
ELECTRON MICROSCOPYf_plane_restr0.00891834
ELECTRON MICROSCOPYf_dihedral_angle_d6.49696422

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