[English] 日本語
Yorodumi
- PDB-8y1o: Cryo-EM structure of human ABCA7 in the apo state -

+
Open data


ID or keywords:

Loading...

-
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 / phospholipid transporter activity / negative regulation of amyloid precursor protein biosynthetic process / ABC transporters in lipid homeostasis / phosphatidylserine floppase activity / floppase activity / positive regulation of phospholipid efflux / amyloid-beta clearance by cellular catabolic process ...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 / positive regulation of phospholipid efflux / amyloid-beta clearance by cellular catabolic process / 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 / apolipoprotein A-I-mediated signaling pathway / regulation of amyloid precursor protein catabolic process / cholesterol efflux / phospholipid translocation / amyloid-beta formation / negative regulation of PERK-mediated unfolded protein response / negative regulation of amyloid-beta formation / regulation of lipid metabolic process / glial cell projection / ATPase-coupled transmembrane transporter activity / positive regulation of cholesterol efflux / protein localization to nucleus / phagocytosis / ABC-type transporter activity / 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
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
Revision 1.0Feb 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
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 %

-
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)

-
Processing

EM softwareName: PHENIX / Category: model refinement
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more