[English] 日本語
![](img/lk-miru.gif)
- PDB-8oxa: Cryo-EM structure of ATP8B1-CDC50A in E2-Pi conformation with occ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8oxa | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of ATP8B1-CDC50A in E2-Pi conformation with occluded PS | |||||||||||||||||||||||||||
![]() |
| |||||||||||||||||||||||||||
![]() | MEMBRANE PROTEIN / lipid transporter autoinhibition P-type ATPase P4-ATPase CDC50A | |||||||||||||||||||||||||||
Function / homology | ![]() vestibulocochlear nerve formation / regulation of plasma membrane organization / regulation of microvillus assembly / positive regulation of phospholipid translocation / phosphatidylcholine flippase activity / aminophospholipid flippase activity / aminophospholipid transport / phosphatidylserine flippase activity / protein localization to endosome / inner ear receptor cell development ...vestibulocochlear nerve formation / regulation of plasma membrane organization / regulation of microvillus assembly / positive regulation of phospholipid translocation / phosphatidylcholine flippase activity / aminophospholipid flippase activity / aminophospholipid transport / phosphatidylserine flippase activity / protein localization to endosome / inner ear receptor cell development / phospholipid-translocating ATPase complex / ATPase-coupled intramembrane lipid transporter activity / phosphatidylserine floppase activity / positive regulation of protein exit from endoplasmic reticulum / xenobiotic transmembrane transport / phosphatidylcholine floppase activity / stereocilium / apical protein localization / bile acid metabolic process / P-type phospholipid transporter / bile acid and bile salt transport / cardiolipin binding / phospholipid translocation / transport vesicle membrane / azurophil granule membrane / Golgi organization / Ion transport by P-type ATPases / specific granule membrane / monoatomic ion transmembrane transport / regulation of chloride transport / sensory perception of sound / trans-Golgi network / positive regulation of neuron projection development / late endosome membrane / early endosome membrane / nuclear body / apical plasma membrane / negative regulation of DNA-templated transcription / Neutrophil degranulation / structural molecule activity / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å | |||||||||||||||||||||||||||
![]() | Dieudonne, T. / Kummerer, F. / Juknaviciute Laursen, M. / Stock, C. / Kock Flygaard, R. / Khalid, S. / Lenoir, G. / Lyons, J.A. / Lindorff-Larsen, K. / Nissen, P. | |||||||||||||||||||||||||||
Funding support | European Union, ![]() ![]() ![]()
| |||||||||||||||||||||||||||
![]() | ![]() Title: Activation and substrate specificity of the human P4-ATPase ATP8B1. Authors: Thibaud Dieudonné / Felix Kümmerer / Michelle Juknaviciute Laursen / Charlott Stock / Rasmus Kock Flygaard / Syma Khalid / Guillaume Lenoir / Joseph A Lyons / Kresten Lindorff-Larsen / Poul Nissen / ![]() ![]() ![]() Abstract: Asymmetric distribution of phospholipids in eukaryotic membranes is essential for cell integrity, signaling pathways, and vesicular trafficking. P4-ATPases, also known as flippases, participate in ...Asymmetric distribution of phospholipids in eukaryotic membranes is essential for cell integrity, signaling pathways, and vesicular trafficking. P4-ATPases, also known as flippases, participate in creating and maintaining this asymmetry through active transport of phospholipids from the exoplasmic to the cytosolic leaflet. Here, we present a total of nine cryo-electron microscopy structures of the human flippase ATP8B1-CDC50A complex at 2.4 to 3.1 Å overall resolution, along with functional and computational studies, addressing the autophosphorylation steps from ATP, substrate recognition and occlusion, as well as a phosphoinositide binding site. We find that the P4-ATPase transport site is occupied by water upon phosphorylation from ATP. Additionally, we identify two different autoinhibited states, a closed and an outward-open conformation. Furthermore, we identify and characterize the PI(3,4,5)P binding site of ATP8B1 in an electropositive pocket between transmembrane segments 5, 7, 8, and 10. Our study also highlights the structural basis of a broad lipid specificity of ATP8B1 and adds phosphatidylinositol as a transport substrate for ATP8B1. We report a critical role of the sn-2 ester bond of glycerophospholipids in substrate recognition by ATP8B1 through conserved S403. These findings provide fundamental insights into ATP8B1 catalytic cycle and regulation, and substrate recognition in P4-ATPases. | |||||||||||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 264.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 205.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 17262MC ![]() 8ox4C ![]() 8ox5C ![]() 8ox6C ![]() 8ox7C ![]() 8ox8C ![]() 8ox9C ![]() 8oxbC ![]() 8oxcC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 136283.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O43520, P-type phospholipid transporter |
---|---|
#2: Protein | Mass: 41085.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 2 types, 3 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#7: Sugar |
-Non-polymers , 4 types, 14 molecules ![](data/chem/img/VN4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/D39.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/D39.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-VN4 / |
---|---|
#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-D39 / ( |
#8: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: ATP8B1-CDC50A complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.185 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: 50 mM MOPS-Tris pH 7, 100 mM KCl, 1 mM DTT, 5 mM MgCl2 supplemented with 0.03 mg.mL-1 LMNG, 0.003 mg.mL-1 CHS, PI(4,5)P2 0.0015 mg.mL-1 and 1 mM Na3VO4 and 0.003 mg.mL-1 POPS |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-
Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 534468 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7PY4 Accession code: 7PY4 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|