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Open data
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Basic information
Entry | Database: PDB / ID: 8y1o | |||||||||||||||||||||
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Title | Cryo-EM structure of human ABCA7 in the apo state | |||||||||||||||||||||
![]() | Phospholipid-transporting ATPase ABCA7 | |||||||||||||||||||||
![]() | LIPID TRANSPORT / phosphalidylserine transporter / lipid flippase / apo-form | |||||||||||||||||||||
Function / homology | ![]() plasma membrane raft organization / apolipoprotein A-I receptor activity / positive regulation of engulfment of apoptotic cell / phospholipid transporter activity / negative regulation of amyloid precursor protein biosynthetic process / ABC transporters in lipid homeostasis / phosphatidylserine floppase activity / 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 / phospholipid transporter activity / negative regulation of amyloid precursor protein biosynthetic process / ABC transporters in lipid homeostasis / phosphatidylserine floppase activity / floppase activity / amyloid-beta clearance by cellular catabolic process / positive regulation of phospholipid efflux / phospholipid efflux / phosphatidylcholine floppase activity / positive regulation of amyloid-beta clearance / negative regulation of endocytosis / high-density lipoprotein particle assembly / positive regulation of protein localization to cell surface / P-type phospholipid transporter / regulation of amyloid precursor protein catabolic process / apolipoprotein A-I-mediated signaling pathway / cholesterol efflux / phospholipid translocation / amyloid-beta formation / negative regulation of amyloid-beta formation / negative regulation of PERK-mediated unfolded protein response / regulation of lipid metabolic process / positive regulation of cholesterol efflux / glial cell projection / ATPase-coupled transmembrane transporter activity / protein localization to nucleus / ABC-type transporter activity / phagocytosis / phagocytic cup / negative regulation of MAPK cascade / positive regulation of phagocytosis / visual learning / ruffle membrane / memory / cell junction / early endosome membrane / positive regulation of ERK1 and ERK2 cascade / Golgi membrane / intracellular membrane-bounded organelle / cell surface / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å | |||||||||||||||||||||
![]() | Fang, S.C. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of human ABCA7 in the apo state Authors: Fang, S.C. / Zhou, C.Z. / Hou, W.T. / Chen, Y. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 328 KB | Display | ![]() |
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PDB format | ![]() | 260.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 366.2 KB | Display | ![]() |
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Full document | ![]() | 389.3 KB | Display | |
Data in XML | ![]() | 36.2 KB | Display | |
Data in CIF | ![]() | 55.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 38841MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 234596.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q8IZY2, P-type phospholipid transporter |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: ABCA7 / Type: COMPLEX / Details: apo-form / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software | Name: PHENIX / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44853 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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