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- PDB-8y1o: Cryo-EM structure of human ABCA7 in the apo state -

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Basic information

Entry
Database: PDB / ID: 8y1o
TitleCryo-EM structure of human ABCA7 in the apo state
ComponentsPhospholipid-transporting ATPase ABCA7
KeywordsLIPID TRANSPORT / phosphalidylserine transporter / lipid flippase / apo-form
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 / 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 / negative regulation of amyloid precursor protein biosynthetic process / phospholipid transporter activity / ABC transporters in lipid homeostasis / phosphatidylserine floppase activity / floppase activity / amyloid-beta clearance by cellular catabolic process / positive regulation of phospholipid efflux / peptide cross-linking / 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 / negative regulation of amyloid-beta formation / negative regulation of PERK-mediated unfolded protein response / amyloid-beta formation / regulation of lipid metabolic process / glial cell projection / positive regulation of cholesterol efflux / ATPase-coupled transmembrane transporter activity / phagocytic cup / protein localization to nucleus / negative regulation of MAPK cascade / phagocytosis / ABC-type transporter activity / 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 / cell surface / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter A / : / ABCA1-like, C-terminal R1 regulatory domain / ABC-2 family transporter protein / ABC-2 type transporter / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...ABC transporter A / : / ABCA1-like, C-terminal R1 regulatory domain / ABC-2 family transporter protein / ABC-2 type transporter / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Phospholipid-transporting ATPase ABCA7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsFang, S.C.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509302 China
CitationJournal: To Be Published
Title: Cryo-EM structure of human ABCA7 in the apo state
Authors: Fang, S.C. / Zhou, C.Z. / Hou, W.T. / Chen, Y.
History
DepositionJan 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipid-transporting ATPase ABCA7


Theoretical massNumber of molelcules
Total (without water)234,5971
Polymers234,5971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Phospholipid-transporting ATPase ABCA7 / ABCA-SSN / ATP-binding cassette sub-family A member 7 / Autoantigen SS-N / Macrophage ABC transporter


Mass: 234596.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCA7 / Production host: Homo sapiens (human)
References: UniProt: Q8IZY2, P-type phospholipid transporter
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: ABCA7 / Type: COMPLEX / Details: apo-form / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44853 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01114567
ELECTRON MICROSCOPYf_angle_d1.31719812
ELECTRON MICROSCOPYf_dihedral_angle_d5.822004
ELECTRON MICROSCOPYf_chiral_restr0.0572258
ELECTRON MICROSCOPYf_plane_restr0.0072544

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