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- EMDB-28050: Cryo-EM structure of human ABCA7 in Digitonin -

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Basic information

Entry
Database: EMDB / ID: EMD-28050
TitleCryo-EM structure of human ABCA7 in Digitonin
Map datahuman ABCA7 in Digitonin
Sample
  • Complex: Human ABCA7 in Digitonin
    • Protein or peptide: Phospholipid-transporting ATPase ABCA7
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / positive regulation of phospholipid efflux / negative regulation of amyloid precursor protein biosynthetic process / ABC transporters in lipid homeostasis / phospholipid efflux / floppase activity / phosphatidylserine floppase activity ...plasma membrane raft organization / apolipoprotein A-I receptor activity / positive regulation of engulfment of apoptotic cell / phospholipid transporter activity / positive regulation of phospholipid efflux / negative regulation of amyloid precursor protein biosynthetic process / ABC transporters in lipid homeostasis / phospholipid efflux / floppase activity / phosphatidylserine floppase activity / high-density lipoprotein particle assembly / positive regulation of amyloid-beta clearance / amyloid-beta clearance by cellular catabolic process / peptide cross-linking / phosphatidylcholine floppase activity / negative regulation of endocytosis / positive regulation of protein localization to cell surface / regulation of amyloid precursor protein catabolic process / P-type phospholipid transporter / cholesterol efflux / apolipoprotein A-I-mediated signaling pathway / phospholipid translocation / phagocytic cup / negative regulation of amyloid-beta formation / negative regulation of MAPK cascade / negative regulation of PERK-mediated unfolded protein response / glial cell projection / amyloid-beta formation / positive regulation of cholesterol efflux / regulation of lipid metabolic process / protein localization to nucleus / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / positive regulation of phagocytosis / 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
ABC-2 family transporter protein / ABC transporter A / 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: 3.9 Å
AuthorsAlam A / Le LTM / Thompson JR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1R21AG069180 United States
CitationJournal: 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
DepositionSep 6, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28050.png

Downloads & links

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Map

FileDownload / File: emd_28050.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman ABCA7 in Digitonin
Voxel sizeX=Y=Z: 0.889 Å
Density
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.029396022 - 0.071222804
Average (Standard dev.)4.4646244e-05 (±0.0016147712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 341.376 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Refinement half map 1

Fileemd_28050_half_map_1.map
AnnotationRefinement half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Refinement half map 2

Fileemd_28050_half_map_2.map
AnnotationRefinement half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human ABCA7 in Digitonin

EntireName: Human ABCA7 in Digitonin
Components
  • Complex: Human ABCA7 in Digitonin
    • Protein or peptide: Phospholipid-transporting ATPase ABCA7
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human ABCA7 in Digitonin

SupramoleculeName: Human ABCA7 in Digitonin / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Details: Human ABCA7 recombinantly expressed in HEK293 TREX cell line and reconstituted in Digitonin
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 234.35 KDa

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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

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration0.5 mg/mL
BufferpH: 7.5 / Details: 25mM HEPES pH 7.5, 150mM NaCl, 0.035% Digitonin
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsHuman ABCA7 in Digitonin

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 60.0 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

9791

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1/4.0)
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1/4.0) / Number images used: 149590

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Atomic model buiding 1

Initial modelPDB ID:

6jbj

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8eeb:
Cryo-EM structure of human ABCA7 in Digitonin

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