+Open data
-Basic information
Entry | Database: PDB / ID: 8ee6 | ||||||
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Title | Cryo-EM Structure of human ABCA7 in PE/Ch nanodiscs | ||||||
Components | Phospholipid-transporting ATPase ABCA7 | ||||||
Keywords | TRANSPORT PROTEIN / ABC transporter / Lipid Transporter / ABC exporter | ||||||
Function / homology | Function and homology information plasma membrane raft organization / apolipoprotein A-I receptor activity / positive regulation of engulfment of apoptotic cell / negative regulation of amyloid precursor protein biosynthetic process / phospholipid transporter activity / ABC transporters in lipid homeostasis / floppase activity / phosphatidylserine floppase activity / amyloid-beta clearance by cellular catabolic process / positive regulation of phospholipid efflux ...plasma membrane raft organization / apolipoprotein A-I receptor activity / positive regulation of engulfment of apoptotic cell / negative regulation of amyloid precursor protein biosynthetic process / phospholipid transporter activity / ABC transporters in lipid homeostasis / floppase activity / phosphatidylserine floppase activity / amyloid-beta clearance by cellular catabolic process / positive regulation of phospholipid efflux / peptide cross-linking / phosphatidylcholine floppase activity / phospholipid efflux / negative regulation of endocytosis / positive regulation of amyloid-beta clearance / high-density lipoprotein particle assembly / positive regulation of protein localization to cell surface / P-type phospholipid transporter / apolipoprotein A-I-mediated signaling pathway / regulation of amyloid precursor protein catabolic process / phospholipid translocation / cholesterol efflux / negative regulation of MAPK cascade / negative regulation of PERK-mediated unfolded protein response / negative regulation of amyloid-beta formation / amyloid-beta formation / glial cell projection / phagocytic cup / regulation of lipid metabolic process / protein localization to nucleus / ATPase-coupled transmembrane transporter activity / positive regulation of cholesterol efflux / ABC-type transporter activity / phagocytosis / positive regulation of phagocytosis / visual learning / memory / ruffle membrane / cell junction / early endosome membrane / positive regulation of ERK1 and ERK2 cascade / Golgi membrane / intracellular membrane-bounded organelle / Golgi apparatus / cell surface / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Alam, A. / Le, L.T.M. / Thompson, J.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: EMBO J / Year: 2023 Title: Cryo-EM structures of human ABCA7 provide insights into its phospholipid translocation mechanisms. Authors: Le Thi My Le / James Robert Thompson / Sepehr Dehghani-Ghahnaviyeh / Shashank Pant / Phuoc Xuan Dang / Jarrod Bradley French / Takahisa Kanikeyo / Emad Tajkhorshid / Amer Alam / Abstract: Phospholipid extrusion by ABC subfamily A (ABCA) exporters is central to cellular physiology, although the specifics of the underlying substrate interactions and transport mechanisms remain poorly ...Phospholipid extrusion by ABC subfamily A (ABCA) exporters is central to cellular physiology, although the specifics of the underlying substrate interactions and transport mechanisms remain poorly resolved at the molecular level. Here we report cryo-EM structures of lipid-embedded human ABCA7 in an open state and in a nucleotide-bound, closed state at resolutions between 3.6 and 4.0 Å. The former reveals an ordered patch of bilayer lipids traversing the transmembrane domain (TMD), while the latter reveals a lipid-free, closed TMD with a small extracellular opening. These structures offer a structural framework for both substrate entry and exit from the ABCA7 TMD and highlight conserved rigid-body motions that underlie the associated conformational transitions. Combined with functional analysis and molecular dynamics (MD) simulations, our data also shed light on lipid partitioning into the ABCA7 TMD and localized membrane perturbations that underlie ABCA7 function and have broader implications for other ABCA family transporters. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ee6.cif.gz | 330.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ee6.ent.gz | 265.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ee6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ee6_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8ee6_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8ee6_validation.xml.gz | 61.8 KB | Display | |
Data in CIF | 8ee6_validation.cif.gz | 90 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/8ee6 ftp://data.pdbj.org/pub/pdb/validation_reports/ee/8ee6 | HTTPS FTP |
-Related structure data
Related structure data | 28047MC 8edwC 8eebC 8eopC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 234598.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABCA7 / Cell line (production host): HEK293TREX / Production host: Homo sapiens (human) References: UniProt: Q8IZY2, P-type phospholipid transporter |
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-Sugars , 3 types, 8 molecules
#2: Polysaccharide | #3: Polysaccharide | beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 22 molecules
#5: Chemical | ChemComp-UNL / Mass: 622.834 Da / Num. of mol.: 20 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION #6: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human ABCA7 in Porcine BPL/Ch/MSP1D1 nanodiscs / Type: COMPLEX Details: Human ABCA7 recombinantly expressed in HEK293 TREX cell line and reconstituted in MSP1D1 nanodiscs comprising 4:1 mixture of Porcine Brain Polar Lipids:Cholesterol Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.234350 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 Details: 25mM HEPES pH 7.5, 150mM NaCl, 5mM ATP gammaS, 10mM Magnesium Chloride |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm |
Image recording | Average exposure time: 60 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50704 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6JBJ | ||||||||||||||||||||||||||||||||||||
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