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- EMDB-38842: Cryo-EM structure of human ABCA7 in DOPS-bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-38842
TitleCryo-EM structure of human ABCA7 in DOPS-bound state
Map data
Sample
  • Complex: ABCA7
    • Protein or peptide: Phospholipid-transporting ATPase ABCA7
  • Ligand: O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine
KeywordsDOPS-bound / lipid transporter / lipid flippase / ABC transporter / LIPID TRANSPORT
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsFang SC
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509302 China
CitationJournal: To Be Published
Title: Cryo-EM structure of human ABCA7 in DOPS-bound state
Authors: Fang SC / Zhou CZ / Hou WT / Chen Y
History
DepositionJan 25, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38842.png

Downloads & links

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Map

FileDownload / File: emd_38842.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.425
Minimum - Maximum-3.7978947 - 5.547204
Average (Standard dev.)-0.002152833 (±0.09233263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38842_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38842_half_map_2.map
Projections & Slices
AxesZYX

Projections

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ABCA7

EntireName: ABCA7
Components
  • Complex: ABCA7
    • Protein or peptide: Phospholipid-transporting ATPase ABCA7
  • Ligand: O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine

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Supramolecule #1: ABCA7

SupramoleculeName: ABCA7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: DOPS-bound ABCA7 complex
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Phospholipid-transporting ATPase ABCA7

MacromoleculeName: Phospholipid-transporting ATPase ABCA7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type phospholipid transporter
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 234.598578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFWTQLMLL LWKNFMYRRR QPVQLLVELL WPLFLFFILV AVRHSHPPLE HHECHFPNKP LPSAGTVPWL QGLICNVNNT CFPQLTPGE EPGRLSNFND SLVSRLLADA RTVLGGASAH RTLAGLGKLI ATLRAARSTA QPQPTKQSPL EPPMLDVAEL L TSLLRTES ...String:
MAFWTQLMLL LWKNFMYRRR QPVQLLVELL WPLFLFFILV AVRHSHPPLE HHECHFPNKP LPSAGTVPWL QGLICNVNNT CFPQLTPGE EPGRLSNFND SLVSRLLADA RTVLGGASAH RTLAGLGKLI ATLRAARSTA QPQPTKQSPL EPPMLDVAEL L TSLLRTES LGLALGQAQE PLHSLLEAAE DLAQELLALR SLVELRALLQ RPRGTSGPLE LLSEALCSVR GPSSTVGPSL NW YEASDLM ELVGQEPESA LPDSSLSPAC SELIGALDSH PLSRLLWRRL KPLILGKLLF APDTPFTRKL MAQVNRTFEE LTL LRDVRE VWEMLGPRIF TFMNDSSNVA MLQRLLQMQD EGRRQPRPGG RDHMEALRSF LDPGSGGYSW QDAHADVGHL VGTL GRVTE CLSLDKLEAA PSEAALVSRA LQLLAEHRFW AGVVFLGPED SSDPTEHPTP DLGPGHVRIK IRMDIDVVTR TNKIR DRFW DPGPAADPLT DLRYVWGGFV YLQDLVERAA VRVLSGANPR AGLYLQQMPY PCYVDDVFLR VLSRSLPLFL TLAWIY SVT LTVKAVVREK ETRLRDTMRA MGLSRAVLWL GWFLSCLGPF LLSAALLVLV LKLGDILPYS HPGVVFLFLA AFAVATV TQ SFLLSAFFSR ANLAAACGGL AYFSLYLPYV LCVAWRDRLP AGGRVAASLL SPVAFGFGCE SLALLEEQGE GAQWHNVG T RPTADVFSLA QVSGLLLLDA ALYGLATWYL EAVCPGQYGI PEPWNFPFRR SYWCGPRPPK SPAPCPTPLD PKVLVEEAP PGLSPGVSVR SLEKRFPGSP QPALRGLSLD FYQGHITAFL GHNGAGKTTT LSILSGLFPP SGGSAFILGH DVRSSMAAIR PHLGVCPQY NVLFDMLTVD EHVWFYGRLK GLSAAVVGPE QDRLLQDVGL VSKQSVQTRH LSGGMQRKLS VAIAFVGGSQ V VILDEPTA GVDPASRRGI WELLLKYREG RTLILSTHHL DEAELLGDRV AVVAGGRLCC CGSPLFLRRH LGSGYYLTLV KA RLPLTTN EKADTDMEGS VDTRQEKKNG SQGSRVGTPQ LLALVQHWVP GARLVEELPH ELVLVLPYTG AHDGSFATLF REL DTRLAE LRLTGYGISD TSLEEIFLKV VEECAADTDM EDGSCGQHLC TGIAGLDVTL RLKMPPQETA LENGEPAGSA PETD QGSGP DAVGRVQGWA LTRQQLQALL LKRFLLARRS RRGLFAQIVL PALFVGLALV FSLIVPPFGH YPALRLSPTM YGAQV SFFS EDAPGDPGRA RLLEALLQEA GLEEPPVQHS SHRFSAPEVP AEVAKVLASG NWTPESPSPA CQCSRPGARR LLPDCP AAA GGPPPPQAVT GSGEVVQNLT GRNLSDFLVK TYPRLVRQGL KTKKWVNEVR YGGFSLGGRD PGLPSGQELG RSVEELW AL LSPLPGGALD RVLKNLTAWA HSLDAQDSLK IWFNNKGWHS MVAFVNRASN AILRAHLPPG PARHAHSITT LNHPLNLT K EQLSEGALMA SSVDVLVSIC VVFAMSFVPA SFTLVLIEER VTRAKHLQLM GGLSPTLYWL GNFLWDMCNY LVPACIVVL IFLAFQQRAY VAPANLPALL LLLLLYGWSI TPLMYPASFF FSVPSTAYVV LTCINLFIGI NGSMATFVLE LFSDQKLQEV SRILKQVFL IFPHFCLGRG LIDMVRNQAM ADAFERLGDR QFQSPLRWEV VGKNLLAMVI QGPLFLLFTL LLQHRSQLLP Q PRVRSLPL LGEEDEDVAR ERERVVQGAT QGDVLVLRNL TKVYRGQRMP AVDRLCLGIP PGECFGLLGV NGAGKTSTFR MV TGDTLAS RGEAVLAGHS VAREPSAAHL SMGYCPQSDA IFELLTGREH LELLARLRGV PEAQVAQTAG SGLARLGLSW YAD RPAGTY SGGNKRKLAT ALALVGDPAV VFLDEPTTGM DPSARRFLWN SLLAVVREGR SVMLTSHSME ECEALCSRLA IMVN GRFRC LGSPQHLKGR FAAGHTLTLR VPAARSQPAA AFVAAEFPGA ELREAHGGRL RFQLPPGGRC ALARVFGELA VHGAE HGVE DFSVSQTMLE EVFLYFSKDQ GKDEDTEEQK EAGVGVDPAP GLQHPKRVSQ FLDDPSTAET VL

UniProtKB: Phospholipid-transporting ATPase ABCA7

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Macromolecule #2: O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy...

MacromoleculeName: O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine
type: ligand / ID: 2 / Number of copies: 2 / Formula: 17F
Molecular weightTheoretical: 788.043 Da
Chemical component information

ChemComp-17F:
O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 473349
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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